Well, I think you played just fine ,AK is very strong hand, no point in folding it preflop so easily.
Okay, that limp-raise could be aces, but I've seen a lot of weak players do it with a whole lot of pocket pairs, AQ etc... no point in expecting aces evrytime you see limp-raise (especially at mico stakes). Not to mention that you have blockers for AA or KK combinations, so the probability that your opponent will always have AA or KK is slightly reduced.
Bad luck that you floped good (top pair, top kicker) and he had aces, but what can you do?
I think that by folding this preflop you lose profit in the long run.