“Some historians point out a pretty basic flaw in the pogrom theory: if pogroms kept people indoors, why wasn’t davening ma’ariv b’yechidus included in the minhag?”
Saliva is Machmits, yet that does not stop those who refrain from gebrox. Many minhagim aren’t that logical.
But to answer your question (trying to use some logic), davening is a lot shorter than learning. With no learning in the shul, there was nothing to do but daven. People returned earlier in the evening, usually while the peasants were still feasting and getting drunk.