Not at all violent per se, but the crushing of the cube Yeoman Thompon in "By Any Other Name" never sat well with me. For me, it made the Kelvins irredeemable, and I didn't care to see them become our friends, as Kirk suggests at the end. To have a character threaten or even attempt to kill people is one thing, but once you have them do it, they've crossed a line that you generally can't un-cross without making some heroic sacrific (i.e. Damar, Doc Ock, or Anakin Skywalker)
And yeah, even though it was painfully obvious the Augment arc could only end with all of them dead and Soong taking up cybernetics instead, Persis' death was unsettlng for me too (Pretty girl deaths usually are, which is probably why slasher films generally aren't my cup of tea).
In terms of gruesomeness, though, nothing beats Remmick. I was pretty young when I first saw it. (I remember the howl that "mother" parasite made REALLY freaked me out!)
Dougherty would probably be a runner up, but I think it was pretty quick on screen and that one screen shot makes it look worse than it was.