Yes, you actually can hurt a person with your thoughts. How would you feel if you were an atheist, and your significant other thought atheists were all delusional thugs? You would feel hurt, not just because they said it but because they're thinking it at all. Sure, a person can conceal their thoughts from you, making you unlikely to be affected by them, but personally, I prefer to be in relationships with people who agree that keeping secrets from your partner is wrong.
Being upset at someone's thoughts is not "thought-policing". It's only thought-policing if you try to control how the other person thinks against their will or try to make them share their thoughts against their will.
Everyone is entitled to their own thoughts, opinions, beliefs, views and feelings (unless they themselves relinquish sole property of those things; which means it's still their choice). On that same token, I am entitled to know the person I'm with and to have the choice of removing myself from a relationship with someone whose thoughts/opinions/beliefs/views/feelings I believe make them a unfit partner. There are thoughts that I believe that only a "bad person" can have. Deal with it.
Hell, you're probably reading this right now and disliking what I'm thinking. Is that the same as policing my thoughts? No. You have an opinion about my opinion. Big deal. Now if you tried to pry more thoughts out of me in a way you know I find intrusive/unacceptable, that would be thought-policing; you are only entitled to know my thoughts if I say you are. If you tried to coerce me into changing my mind, that would be thought-policing. Again; you have no authority over my thoughts unless I say you do.
There is a big difference between thought-policing and simply wanting to make an educated decision about what kind of person you're choosing to be with. There's more to a person than just their behavior; a lot can be said about their character based on what goes on in that head of theirs. Also, it's not abuse if the person permits it, likes it, and gains genuine happiness from it. That's why I prefer to be with people who agree that partners should NEVER keep thoughts (or anything) from one another. That way we can skip past the whole "abusive" and "boundary-crossing" mess and it can just be a mutually healthy and consensual decision for us.
If you think thought-policing is merely being angry at/hurt by/disapproving of someone's thoughts and/or choosing not to be with them because of the thoughts they express/don't express, then congratulations: You're one of those hypocrites who wants to be able to enter/exit relationships for whatever reason you damn well please, yet you don't want others to have that right as well.
In fact, trying to discourage me from feeling/thinking whatever I feel/think about someone else's thoughts actually does constitute as thought-policing.
I wonder what form of abuse it is to tell me that I don't have the right to exit/refuse a relationship with someone who has (by my standards) poor character.