Wouldn't my character therefore start to see him as not being evil? I'm not sure it would have been such bad rp on my part if this had happened. Nor on his, for that matter, since I can't see why an evil wouldn't such up to someone useful to him, like a transmuter.

I would say that if it gets to the point where your good character doesn't see anything wrong with an evil character, then at least one of you isn't roleplaying. I would see the evil character USING a good character... but not showing him respect or returning any kindness. You're thinking too logically, from the standpoint of a neutral player. While it might be beneficial to suck up to a good healer, most evil characters are still going to have evil tendancies that are going to override the logic. Besides, if you follow the logic that being nice to people is more useful then using and abusing them, then aren't you already acting neutral? As the good person in this equation, you should be concerned about how the evil character is using you, questioning his intentions, etc.