This is what they do in Wakfu.

While mining/farming you sometimes get teleported into a fight where you must click on tiles that match the enemy tiles. The tiles are animated so its harder for bots to get around it. If you win you get a x20-x40 of the resource you were gathering. If you fail you get a debuff for some time that decreases your farmed resource yield.
Runescape used to have these random spawns when you were fishing/woodcutting and very often you could see bots get killed.

I'd love to hear about any other games that have done bot prevention without hurting regular players.