Second-guessing yourself at every step is classic self-sabotage, just write it as well as you can and then (after a few weeks' gap) read it back to yourself, or get someone whose opinions you respect to read it.
Violence is the last refuge of the incompetent.
Is that sadistic choice something you think everyone hates and is sick of by now or something that you yourself hate and are sick of? I personally don't have a problem seeing it and it works in superhero type things and other types of stories. I can't tell you if you did it well or not, though, since I haven't read it.
Cheesus!
Don't let Fridge Logic set in and you're good.
If you're worried about people thinking it's overdone, you can add a bit of novelty to the use of the trope if you have the hero make an unexpected choice—probably "I choose to kill you", though you might be able to pull off "shooting you takes a second and I can still save them" (taking a third option is pretty common, but maybe not so much for this kind of thing) or having the protagonist be paralysed by indecision and lose their chance at either (the wrong kind of third option, oops).
I don't think it's such an overused thing that it would ruin the story if you manage to make readers invested in the situation and outcome, though. Make sure it makes sense, and commit to the consequences, and focus on good writing rather than specific considerations about the trope, and you can get away with pretty much anything.
You will not go to space today.
So during the climax of my story, the villain gives the hero the classic. "Stay here and kill me, or go and save your friends" line. Now obviously this is one of the most hack cliches out there, but unfortuneately, it fits the character and scene perfectly. The villain is a sadistic Manipulative Bastard and why I as a writer don't like it, NOT having the villain do this would feel OOC at this point.
So how do I use a Sadistic Choice without the readers crying "Cheese!"