That's probably my fault.
I agree that It violates the be-nice policy. When handling comment flags, you're given 2 buttons, and they're both negative d-words: "decline" and "delete". I clicked on the wrong one.
I had realized after the fact, I clicked on the wrong one, but at the time, I had this notion that this was a user who wasn't familiar with the purpose of the site, so I decided to respond to his comment instead.
Again, I'm sorry. It was totally my fault. If I could go back and do it differently, I would.
As a note, comment flags are kinda lumped in with the flags on the question, and other moderation-related notes, so I can understand how it could have looked to Philipp like a flag on the question.