It could still work just fine. Right now on our server Ceru are the ones that own the town. Sooo many of them it's like a 10 to 1. I think the easy solution here is base off how bad the unbalance is. Aka, give buffs if your faction isn't as large as the others so even if you meet a group of them ~ you can still defend your self. Pvp is fun, but only if it's balance in some way. Most games figure out it's best NOT to have factions so that way more people are in combat making the fair value base off your friends or clans instead. That or class base fairness.
On the other hand, other games give buffs. For the faction that is lower, they give a pvp buff equal to how low they are. Meaning, if the balance was off 80%, then they give the player almost god like powers to combat that. That way a group of them can't just go on a witch hunt for non faction members. On the other hand, it makes playing pvp areas like SSP harder, and in some cases, either require or give the others players a reason to join lower pop team for the extra powers or better rewards.
Ways to promote more players on the other team in a good pvp way even if there are bots:
1) Require faction choice on joining a pvp arena instead. This keeps bots from just taking places form real players. Even if they join the pvp area, they MOST fight to gain points or risk being kick from the game. This is a easy way for games devs to find bots and some games use this tactic.
2) Rewards base on faction levels within an area. Another way is to allow lower pop factions access to points even if they can't really do anything about it. A steady stream of points might take longer to get, but still an option to get points is way better than no option at all. Did you at least attack the other faction? Did you at least hit them? Did you bla bla bla - should still count for a number of points. This will also keep bots from benefiting or force them to combat if they want the points.
3) Give buffs base off faction levels. If your faction is a lower pop by lets say 20% with in the area that is also wearing the faction clothes ~ then you get a 20% boost on your states within that area as well. This way it'll take that many more players to destroy you forcing more pvp in that area for the other faction. In return for this, (as I believe in a give an take system) they have higher death timers, aka it takes them long to revive, so they can't just keep griefing or using their powers to mess with people if they do lose.