Is there a polite way to rescind a request for recommendation letter?
The key thing here is that you say that you have stronger letters already. If you no longer need him to write a letter, just reply to your own email to him saying you don't need one anymore. Something like this should do:


  "Thank you so much for agreeing to the write the letter. Another professor just got back to me about writing a letter so I should be all set for letters in this round of applications. I really appreciate your offer and I will be in touch in the future if I need one though. Thanks again!"


Keep in mind that most people won't write a letter until they have a deadline in front of them. That said,  it is certainly more polite to let any potential letter writer know as soon as you know you won't need it just as it is polite to let them know well advance of when you will.

You frame this question as about "rescinding" a request and seem to be worried that the professor is going to be upset. You should understand that for professors, writing letters of recommendations is a thankless chore. Although this is generally the case, it is particularly the case for undergraduates that we only know through a single class.

Writing these letters takes hours on aggregate. Worst of all, because we also sit on the committees that read these applications, we are also all deeply aware that the letters will be read by a few people on a graduate admission committee if we are lucky.

Seriously though, he is not going to hold it against you. By agreeing to write a letter in the first place, he was offering to do you a favor. By letting him off the hook, you are doing him one.

Although it's not part of your question, I think you are spending too much time trying to unpack and interpret what really happened. Maybe he was busy or in a bad mood? Maybe he was emailing with somebody else and was confused? You say that you don't want to second guess him but that is exactly what you're doing. If he encouraged you to apply for a PhD program and said he will write a letter, it seems extremely unlikely that he's trying to sabotage you.