Currently, it is easy to defend faction warfare plex with afk alt bots - just get an alt with unfitted ship inside plex and leave it there for 10/15 minutes while attackers have to shoot rats constantly. Even if someone find and kill it - you’ll lose few hudred thousands ISK just, which is nothing comparing with potential gain (up to 40k LP that translates roughly into 40 mil ISK at least). And in certain timezones it can be fully safe as opposing faction don’t have enough people to hunt these. Even if there are some enemies - you can use cheap dual-plate punishers for this and survive long enough to bring your alts fleet to defend it.
So, my ideas how to deal with that:
Make defender to sit in 5km radius of warp-in point beacon to defend it. Respawn the beacon 15km away from current location every minute (current 30km circle of zone border can be used for this, so beacons will be not far from center of the plex). So,defender will have to move ship every minute using at least AB (no unfitted ships can do it anymore). Also, both defenders and attackers will have to move through zone constantly too if they want to stay at their optimals to warp-in point. This will make life for botters harder without huge stress on active players.
Make a list of currently contested plexes in warzone, so people can read where they needed most and afk botters will have more troubles to defend plexes.