There are different principles motivating each intuition, I think. The first intuition is motivated by the principle that no one should be compelled to do something that they would not freely will. Though this is clearly not an exceptionless principle, it's a generally good one. You can't force someone to do something they don't want to, unless you have good reason. Problematically, of course, prisoners are such that we already have good reason to force them to things they don't want to do: as they have violated our laws (or, at least, been convicted of violating the laws), then they are forced to lose certain freedoms and have their behaviour monitored closely. This reason is not, however, a carte blanche: inmates can't be forced to do anything, just because they are inmates.
The second intuition is motivated by the principle that one should be able to act on one's freely-willed decisions. Again, this is not exceptionless, but generally good. We can't prevent people from acting on whatever decisions that have freely arrived at unless we have some good reason to do so. Again, problematically, prisoners are already being interfered with, but only to a certain extent.
So, really, it looks like the conflict I'm having here can be resolved if there's some good reason to allow extending the interference inherent to the life of a prisoner such that they can be compelled to participate in medical trials, or if there's some good reason to refrain from extending that interference such that they cannot be prevented from participating in medical trials. Generally, I would think that there is no good reason to force someone to participate in a medical trial. That is literally gambling with their life, and I can't think of a single reason for compelling someone to risk their life against their will. So, there could only be good reason to stop inmates from participating. One, which is raised in the article, is a concern for the inmate's future health. Another may be the possibility of coercion. But, as long as coercion can be ruled out, and as long as inmates are informed about the risks of the trial, then there seems to be no reason to prevent them from engaging in medical trials.