Yeah, you'll get callouses on both hands.

My only other thought is that with your fretting hand you might be using too much pressure - causing the pain. I think everyone I have ever taught (including me) has been guilty of this. If you haven't already, spend a session just finding out how little pressure it takes to get a note to sound.

You get used to wrestling the guitar when you start, but when your figers are tougher and you've gathered some technique, you don't need to hold the neck so tight....

Just a thought...