First, yes, but that's the way writing works. That's the reason anything happens in Mass Effect: the writer made it happen through their own contrived rules, every last one of them.
No, that's how
bad writing works. If something just happens because the author clearly wants it to happen so it'll happen no matter how little sense it makes in the context of everything else then it's bad writing. With good writing it all flows together so feels natural, even though it's probably been worked out very, very carefully.
Second, no, style over substance would be a conventional/military victory. I know better than to discuss the "substance" here to any degree, but it's certainly not the most egregious presentation of style over substance that could have come out of the situation.
That would be another example of style over substance. The possibility of other means of having it doesn't mean that this wasn't.
Third, "the whole Jesus thing" is all about the question posed to Shepard about the organic-synthetic conflict, The Reapers' purpose of creation, and the path the galaxy needs to take next, along with their sacrifice to enact the decision. One can make the complaint about "moody and meaningful" in any piece of fiction they don't like where the character dies.
And he's got to give his life (probably) for it? Please... It's bad enough that it'll boil down to one person on the spot.
If it's the only reason for the character dying then you can indeed make the complaint in any piece of fiction, entirely validly.
FWIW I've always read the intention of high EMS Destroy to be "Shepard survives", just done in an incredibly bad and unsatisfying way.