Yes, the owner of the club can probably ban you from entering if your significant other works there (or for any number of other reasons). You may have seen signs in different establishments that say "We reserve the right to refuse service to anyone." As long as you are not being kept out on the basis of your race, religion, national origin, or on the basis of your membership to some other protected class, you are not actually being discriminated against and you can be kept from entering. As a private club the owner is given much more leeway in determining who enters than is allowed for public areas.
As you have already discovered, while all clubs have the right to refuse you entrance based on your relationship, not all do. Rather than seeking legal action you will probably be better off talking to your girlfriend about working at another club with different rules.