It will be virtually impossible to have a solid solution, since auto clickers emulate hardware. Unless you can figure out a way to detect that the player is using one without imposing some arbitrary limits on the number of clicks, or adding annoying things to the game - then you won't really be able to stop anyone from using an auto clicker.
I personally have a mutant/abnormal ability to click a button very fast (280 clicks in 25 seconds - or an average of 11.2 clicks per second). I've seen people as fast as 16 clicks per second... Most auto clickers have adjustment on them, so a player can find the "sweet spot" and just set it to that.
The only thing I can think of that MIGHT work is measuring the time between each individual click - then if the time is EXACTLY the same for say 20-30 clicks in a row (2-3 seconds worth?) then you can trigger an "auto clicker is being used" event and stop your game - or whatever. That's about the only way I suspect you could do it actually. That's the thing about auto clickers, I don't think they vary the time between clicks at all; they're very uniform.
~Sol