The night the dark mark was cast upon the astronomy tower in Half-Blood Prince, Professor Snape stunned Professor Flitwick before joining the battle.
“Outside Snape’s office, yes,” whispered Hermione, her eyes sparkling with tears, “with Luna. [. . . .] It was nearly midnight when Professor Flitwick came sprinting down into the dungeons. He was shouting about Death Eaters in the castle, I don’t think he really registered that Luna and I were there at all, he just burst his way into Snape’s office and we heard him saying that Snape had to go back with him and help and then we heard a loud thump and Snape came hurtling out of his room and he saw us and — and — [. . . .] “I was so stupid, Harry!” said Hermione in a high- pitched whisper. “He said Professor Flitwick had collapsed and that we should go and take care of him while — he while he went to help fight the Death Eaters —” [. . . .] “We went into his office to see if we could help Professor Flitwick and found him unconscious on the floor . . . and oh, it’s so obvious now, Snape must have Stupefied Flitwick, but we didn’t realize, Harry, we didn’t realize, we just let Snape go!”
There were no Death Eaters there to witness, so Snape didn't need to attack Flitwick to act his part. He also didn't stun Hermione and Luna, which would have made sense if he was trying to keep as many innocent people away from the fight as possible. So why?