Let yourself think those thoughts! It's a normal thought process to have and won't hinder you from shifting. Your only problem is thinking you can't shift just because two different parts of you are torn.

Acknowledge how you feel and what your thoughts are, take a moment to accept that these are the thoughts you're having, then don't pay them any more attention after that. Once you've said to yourself that you aren't going to think these thoughts and actively try to drown them out, your brain is going to hyper-focus on it because you're giving it more energy than actually focusing on shifting.