A flop check-raise can mean numerous things in this instance; you have no reason to assign villain an A based on the action thus far. Villain's check-raise may be for protection purposes (assuming he thought MP1 would auto-bet the flop) when he holds medium/high pocket pair or, as you've stated, to extract value out of flush draw, etc.

I think 3-betting the flop is your best option here, since a turn raise will scare off CO, who is likely drawing near dead (unless, of course, he's holding a flush draw). In my opinion, 3-betting the flop kinda under represents your hand and may entice calls. If villain caps then I think you should consider reverting to call down mode.

Based on the action, folding is out of the question in my opinion.