I don't see this as a big deal. Words can have multiple meanings - "temple" for instance also means "flat part of the side of one's head."
Even when "fane" means temple, it's typically used to connote "evil temple" specifically.
Because saint has become associated with good by connotation. Yes, you can technically have evil saints, or evil religions that consider themselves holy and the good religions unholy, but in a gaming context you'll almost never see those usages applied that way.