The problem with that line of thinking is the reality that almost everyone who is in prison is a predator of some kind or another, and everyone is a potential prey to the others. Like, if you have 100 murderers in a prison, each of them are predators but also potential prey to the others.
We can do some mitigation, though, such as not enabling more chances to do evil. E.g., they can't drive around the prison, so they have no more chances to kill someone in a DWI accident.
In the case of men vs women, the problem is really more complicated than just not putting women together with the rapists. (Which, incidentally, has happened repeatedly.) It's also that, as I've said in the sports discussion, women are on average biologically weaker than men. It's not just muscle mass, but also, as I've pointed out before, slower muscle contraction speed, different composition of muscle fibres, weaker skeleton, etc. And resulting issues, like higher chance of a concussion or fracture for the woman if an average male were to fight an average woman. The fight-or-flight response is also well documented to be different, and supported by MRI studies.
The short version is that if you put a woman in a cell with a guy convicted of assault or worse yet murder, even if they're convicted of the same crime, the guy can dominate and abuse the woman six ways to Sunday without even being particularly buff. Even without him actually be convicted of a rape or such, the woman is put in a dangerous position.