New continuity (and old continuity too iirc) had Freeze using human subjects, despite having the resources of a full lab. That's why he was fired and turned to crime. Batman worked in rehabilitating Clayface, Red Hood, Cassandra, etc. If given the opportunity he will work with and help the villains (except maybe Joker, even if he becomes sane he's done too much). That's why he sends them to Arkham Asylum, a mental institution he contributes a significant amount of resources that go into security, research, and top psychiatrists, and not to Blackgate, a prison that won't offer any help.

Freeze is delusional and, like you said willing to do whatever it takes to cure his wife. Even if that includes kidnapping people and giving them the disease.