It’s derived from the noun “guy”, which is indeed often gendered. But etymology doesn’t determine meaning. Otherwise we would have to conclude that “woman” is male-gendered because it etymologically derives from “man”.
Making “you guys” taboo seems to be a cultural phenomenon specific to certain industries. I’ve asked several of my friends, and never encountered one outside of tech or academia who thought “you guys” was problematic at all. In fact, the vast majority had never even heard of the issue or imagined that it could be controversial.