First of all I am going to consider which is more likely if Justine regains her pre-illness form, and Venus continues to show the renewed confidence and commitment(although I do believe the commitment was there before Wimbledon this year, it was the former lacking)she showed in the second half of this year. If Venus continues to show the form she showed Wimbledon onwards, and Justine does not regain her pre-illness form it is a no-brainer. If both are able to play quite a few more years at full health, confidence, and peak form, it is something to think about.
Venus was the best clay courter in the World in 1999 going into the French Open. Her impressive performances included titles at Hamburg and the Italian Open. In the Hamburg final she defeated Mary Pierce, an excellent clay courter, 6-3, 6-0, in the Italian Open she beat then world #1 Hingis in the semis in 3 sets, and Pierce 6-4, 6-2 in the final. She was the slight favorite over Hingis and Seles to win the French Open that year, but was shocked by a red hot Barbara Schwarz in the 4th round, one match before her expected meeting with Hingis in the quarters. There are 5 high caliber tier 1 or 2 clay court events leading into the French Open each year, I consider them about equal in caliber of field and importance, to the point I have to remind myself which 3 are considered the tier 1s; Amelia Island, Charleston, Roma, Warsaw, and Berlin. She never plays more than 3, usually 2, and won atleast one of those five tier 1/2 caliber clay court events in 1999, 2001, 2002, and 2004; was coming off a long injury layoff during the leadup tier 1/2 events in 2000, and was injured in 2003. In short she has shown more promise on clay in the bigger pre-French Open tournaments than her French Open record-one lone final in 2002, and 3 other quarterfinals.
On grass there are fewer tournaments obviously, there is almost only Wimbledon to go by for the women, although some play Eastbourne, it is a less significant tournament than any of the 5 pre-French Open warmups for women. Henin actually has a very good record at Wimbledon as BitterBlueBong pointed out. A final, and two semis, in three years straight from 2001-2003, easily trumps Venus's best multi-year French Open run. She also has a disaesterous first round loss as a top player, something Venus had in 2002 at the French as the #2 seed as well. So based on performances by Henin at Wimbledon vs Venus at the French, Henin has put together a multi-year run easily besting Venus at the French; but as I said Venus has shown more potential on clay than her French Open results have converted.
It is interesting to look at how each did against other top players on the surfaces. Venus's past meetings with Henin on clay make me think rather little of her chances vs Henin on clay on a typical day, in a year both are healthy and confident. Yes their head to head is 1-1, but she lost the first meeting 6-4, 6-1 in 2002; and was down 6-2, 4-0 in their second meeting before according to all reports Henin choked big time, something she was liable to do pre-2003, but a win is a win. Yet she has never lost to her on any other surface, although all their meetings were in 2001-early 2003. As well Henin in 2001-2002 was not near the player of 2003-2004, so all indications would be Henin is not a good matchup for her on clay, unless she is in red hot form and making almost no UEs. Of course Venus with her game style could probably still win if she were clicking on all cylinders, but that is what would be neccessary for her to beat Henin on clay I believe.
Against Clijsters her only meeting on clay was a 1-6, 6-3, 6-4 loss, going on one match is not as good an indicator as two matches, especialy if it close, it is quite conceivable a player had an off day, or it was an minority outcome, or some other variable. Clijsters, like Henin was not nearly the player in 2001-2002 she was in 2003-2005, but given that it was only one match, I wont read much into it, and since Venus won the first set 6-1, she probably really should have won the match that day. Very impressive too is a 3-0 vs Mary Pierce on clay, all those matches when Pierce was established as a top 5/top 10 player over a substained period of many years, not a surprise contender like this year; keep in mind Pierce is now a 3-time French finalist, a French Open Champion in 2000, a many time tier 1 event winner on clay, and she is much more of a specialist on slower surfaces than faster ones. She never finished a match vs Mauresmo on clay, retiring with an injury while down in the 3rd set of one, a legit injury IMO, not much to go by at all there. She is 0-1 vs Serena on clay, losing in the 2002 French final, during a string she lost 6 straight times to Serena on a variety of surfaces anyway; and 0-1 vs Davenport on clay, their only meeting ever in the Amelia Island quarters, a 3 set win for Davenport during a period she won 4 straight times over Venus on a variety of surfaces anyway as well. She smoked Dementieva in their one meeting on clay in Fed Cup this year. She has never played Sharapova on clay. She beat Kuznetsova convincingly in the 2004 Warsaw final, and Kuznetsova had match points on the eventual champ in the last two French Opens. I would say there is little evidence how she fares vs Davenport, Serena, Mauresmo, Sharapova or Clijsters. Indications are Henin has a clear advantage over Venus in a head to head on clay, but Venus having an obvious advantage vs Pierce, Dementieva, or Kuznetsova. All in all she seems able to hold her own vs any of the top players on clay, except for Henin, so far.
Just for what its worth it is interesting to look at how she did vs some past quality contenders on clay, which are meaningless as far as her opposition to a French title now, but interesting for whatever influence they have on your accessment of the degree of her clay court ability. Against Hingis she is 2-2 on clay, very impressive considering Hingis despite not winning the French Open was considered a quality clay courter, better than Venus on clay in some peoples eyes. She is 1-0 vs Seles on clay, beating her 6-4, 6-3, when Seles had upset her in the Australian Open quarters that same year. She is also 1-0 vs Martinez on clay, a 3 set win over aging Martinez last year in the Charleston final, not much to tell there. She is 2-2 vs Sanchez Vicario on clay, extremely impressive vs one of the great clay court players of the last 15 years, who was still a contender on tour during those years. Her head to heads vs past quality clay courters is quite good as well.
Justine on the other hand is 0-1 vs Serena on grass, a 6-3, 6-2 thumping a month after her win over Serena in the French Open semis. She is 0-2 vs Venus on grass, a 6-3, 6-2 thumping in the 2002 Wimbledon semis, when she had taken Venus to 3 sets in 4 of their last 5 meetings; and a 6-1, 3-6, 6-0 loss in the 2001 Wimbledon final, and believe me that match was not close in the least, despite Henin winning the 2nd set, Henin looked pretty severely overmatched the whole way, and used some bold net approaches that surprised Venus and a bit of a loss of focus from Venus to take that 2nd set. She has never played Davenport on grass, nor Sharapova. Her best wins on grass are a win over Capriati in the 2001 Wimbledon semis, a 3-setter, after Capriati had beaten Serena in the previous round, and after Capriati had won the first 2 slams of the year; and a win over Monica Seles, who she had lost to 4 times in a row and had never beaten at that time, in the 2002 Wimbledon quarters. Ability to fare well vs the leading contender on grass I would say is minimal so far, and far less than Venus on clay. She has not been around long enough, or been ranked that highly for enough years, to find any head to heads vs the last generation of top players either.
I would have to say overall Venus has the better chance to pull out a French Open than Justine the French even if Justine regains her pre-illness form.