“Why couldn’t they establish a much better Minhag, to stay in Beis Medrash all night just light Shavuos? “
Because we’d be a bigger, easier target with the lights on in a large building.
_________________
“One more question I have is, aren’t we talking about a ghetto? What are Goyim doing there?”
They could walk in any time they wanted. They were free in their country. We were considered the tolerated (at best) minority.
__________________
“…being bothered by an ancient Minhag Yisroel is unacceptable.”
What do you mean by ancient? What is the earliest source? When I think of ancient, I think of at least 500 years, actually 1000+. But maybe you have a different understanding.
Before you said, “It was not in Sefarim for obvious reasons.” That does not sit well with me, as one can say that about anything, like the blood libel.