So, having once offended, even quality, dare I say even humble, comments by that user should be flagged? Were you not autoflagging him, you would not be likely to have flagged that comment, and since you have automated your opinion, you have not potentiated engagement and disable rapprochement.
You may be fine with that. Upon reflection, you may not be. Can't speak for you, but you are now the kinda guy that flags people that say nice things about you despite having been flagged hard by you for a long time. He's clearly showing integrity despite his hard feelings. Maybe you don't have a moral bone in your body, but your avatar did, and that's not something he'd have done.
A comment like that in these circumstances deserves a personal reply, not an autoflag. Society is people, not bots. You're not a bot. Don't let a bot act for you and determine your socialization.
Or, do you. I reckon you're better than that, but you will decide.