If Blizz is planning a ban wave at the end of Season 2 then it's unlikely that they'll wait to the very end to start looking for bots. Whether your account is flagged or not, stopping now won't change much.
Of course, there's no telling for sure how they detect D3 bots. If they can detect the mere presence of the bot controlling the game then your only hope is that your account is one of the detected ones that doesn't get banned (they don't ban 100% of detections for obvious reasons).
On the other hand, if they're detecting bots with some kind of statistical data then it's possible that they'll pay more attention during the xp boost looking for people going 24-7 or something. Who knows.
Personally I'm not stopping, but at the same time I'm not botting 24-7. I don't think it'll save my account or anything, I just want to see if I still get banned even when I'm not being abusive with the bot. If I do get banned, no big loss.