I don't think you overreacted. He thinks you're pretty, he asked if you minded the nickname "beautiful", you said "yes". Maybe he started the chat to see if you guys still had a good working relationship and to be sure he didn't offend you. So as long as he doesn't continue/escalate, you're fine.
Every guy who compliments a woman isn't a rapist who needs to be beaten with a flaming hard copy of GOF.
And I don't see where anyone is suggesting that. That being said, there is no need for this guy to ever comment on anything about the OP in a professional environment outside of her professionalism. I seriously doubt he's going around commenting on the physical appearance of everyone he emails business with.
If he thinks she's pretty, then so be it. He can tell her in a setting outside of work.
The correct response from him was to reply with "I apologize and I won't do it again" then never mentioning it again. Chatting to see if everything is ok, is not ok. It doesn't mean that anyone thinks he's going to violate the OP, but it does mean that his behavior is inappropriate and unprofessional. It's best for the OP to be very clear that she doesn't want to communicate with him if it doesn't 100% involve her work.