If you can't (or won't) remove the problem, remove some of the reasons.
I got to thinking about WHY bots flock to dungeon bosses. I know players farm them for specific drops or lots of whites for deconstruction, but once their bags are full, they leave. Bots don't. It's not effective for them to leave and return and it's much more difficult to automate so they can run unsupervised. Here are some of the reasons I think they're there, and easily implemented solutions to make it less worthwhile.
1) Exp
Fast fixed-spot respawn and (I think) larger than usual exp per kill, making it the obvious spot to bot level raises
SOLUTION: Make dungeon bosses give zero exp for kill, and raise the 'first kill/dungeon complete' bonus to compensate
2) Cash
They don't drop much gold, but they do drop soulstones. These sell for a comparatively large amount and stack to 100, meaning it's a steady cashflow income without having to worry about running low on space. 4 bots, 15g per ~30s, over 7k per hour, 170k for running a set of bots in one dungeon for 24h
SOLUTION: Soulstones sell for 0g, like so much other stuff in the game. Players can still farm them for use (rez/charge) but they aren't a disproportionately large ticket cash item
Both of these solutions are trivially easy to implement, look to have no obvious problems with conflicts in a complex system, and have negligible effect on the legitimate player base.
I know it won't solve the problem, but I believe it would go some way to moving them on from the industrial-scale automation they're currently engaged in.