Well the comments coming from the author seem a bit passive-agressive in my opinion.
I think if you are inconfortable with some comments your readers made, just tell them nicely, and if you have a lot of comments that makes you inconfortable, just make a small announcement saying that you're not mad at them but it's making you a bit inconfortable so you'd like them to stop. And usually, they apologize and stop, you don't have to be mean about it.
I also agree with @Marvin about the fact that when your readers start shipping and making silly theories, it means that they really like your story and are engaged in it.