Lower Decks was always supposed to be Trek's Beavis and Butthead or South Park or raunchy "adult" shows along that line (personally I find those more juvenile than adult, but whatever). These shows sell. It's a specific brand of humor that a lot of people obviously like, but before this week fans who didn't prefer it could sort of compartmentalize SNW and LD as separate things and skip LD entirely (which I did after giving it a fair chance for 4.5 episodes).
Then the showrunners went all in on that for the SNW/LD crossover, and that's their right too. I think it's brought out vicious debates because LD is a love it/hate it thing. There's not a lot of in-between. Even Jar-Jar Binks has a lot of SW fans that sort of just accept he's there, and when Jar-Jar did show up in shows like the Clone Wars (or even have entire episodes revolving around him), his more excessive elements were toned down (for example, Jar-Jar did a much better job at keeping his cover posing as Boss Lyonie in front of Grievous for most of TCW episode 'Shadow Warrior', while Boimler couldn't even maintain his boundaries on the Temporal Prime Directive for a few minutes). Even when Jar Jar was paired with Mace Windu in TCW Season 6, Jar-Jar fared well enough that even Mace admitted, "Wesa won" at the end.
Boimler is the punch guy of the jokes, everyone looks down on him, and Pike condescendingly told him he's going to the brig and then a starbase to "be someone else's problem". Maybe people like beating up on the outcast or the one out of place and find that funny, and going by the tone of these boards I can already tell those types of people. I don't find it funny.