A limp with a KK is so odd, i just wonder how the fellow had been playing before. Was he really a calling station? Or did he normally bet out with lesser hands, trying to take pots down early? Yes, a VPIP of 50% is crazy-- but over what period of time? how many hands? He could have been on a streak of great hands and was simply tired of raising and having everyone fold.
Did you play it badly? Well, you were SB and it doesn't suck to complete the A9s. Then when the flop comes and gives you some nice draws, I have no problem with you betting out here. He did nothing to alert you at that point -- could have had anything from one pair to the nuts. On the turn, when he raised-- that's where your antennae should have gone up. You still had nothing and the board could have made your still-incomplete draws worthless. Calling a re-raise here... ummm. I'd say no, depending on your read of him from other plays. Does he bluff much at pots? If he has been bluffing
at dangerous boards, a raise to his re-raise could have been interesting.
Given how he played it, without knowing a lot more about him, there is no reason to believe he had KK here. Could as easily had QJ or JT -- either of which is the sort of hand some people call with UTG. Both, of course, beat whatever you could draw.