The thing to consider is that having an illness will generally only decrease a person's stamina simply because the body is just using more energy to cure itself, so Kimmimaro being healthy only means that he would be able to last significantly longer than when he was sick.
Also, Lee at the time was considered to be much weaker than before, having just recovered from a life-threatening surgery and hardly opened the first gate to try to use the initial lotus. Even Gaara said himself that Lee was much stronger back when they fought the chuunin exams.
The last thing to consider is that Gaara did not utilize the power of Shukaku. As a jinchuuriki, Gaara's greatest power at that time, was his ability to call on the power of Shukaku to gain immense power over his foes.
When factoring all of these other variables into what would happen in an actual fight between Kimmimaro and Gaara/Lee without any inhibitions, Kimmimaro's chances of survival seem to decrease significantly, though if you are only referring to only Kimmimaro having a stamina boost from being healthy, then his chances of winning are tilted more in his favor as he would have likely killed either Gaara or Lee back then.
