Board Thread:Questions and Answers/@comment-27852551-20160223093522/@comment-27701762-20160223094553

Killing Flowey at the end does not count against your Pacifist playthrough. It couldn't, in fact, since you will reload a save from before you killed Flowey, nullifying the act itself (you could test it out yourself if you wanted to by saving, killing some enemies, and then quitting and reloading; or at least you could test it out if you had an extra save file). So long as you've fulfilled the baseline criteria for the True Pacifist ending, you'll be able to reload the game and get the ending.

The only argument against killing Flowey at this stage is as confirmation that you've done everything, since Flowey will give you a hint about what to do next to get the True Pacifist ending.

It's your decision, though.