It is a genuine issue, but faction locking is not the answer.
As for why I know it’s a genuine issue, my home server in vanilla was heavily horde-leaning. Eventually, free transfer was opened for alliance and nearly all of their top guilds left the server. Alliance on the server was left with maybe 1 or 2 guilds who even think about Naxx. By endgame, there was no world PvP because there was no alliance.
There is no easy fix though. Balance issues in realms led to cross-realm battlegrounds in the first place too, followed by cross-realm instances in later expansions, and while the former is OK, the latter is a huge no-no.