It"s easy to be scared of a flopped A when we have KK, however need to understand how many Aces villain has in his range that he"s willing to call a 3bet out of position with. If he opens with AK from a stack of 40x, is he likely to 4bet shove over your 3bet, or is he a conservative or trappy player? If he opens with A2-AQ, is he likely to be bad enough to flat call oop - imo most decent players would fold or shove in that spot from a 40x stack, and flatting with a hand that might be crushed is sub-optimal. Factor in how many times he opens with a smaller pair, or suited connectors, and then calls your 3b with implied odds.
So, assuming he is a good player (good or bad assumption, but without any other reads, I"ll assume worst case and that he"s good), the sort of range I would expect him to open, then call a 3bet out of position with (even though implied odds are wrong for set mining in your example), might be AK, 22-TT (assuming he 4bets JJ+) and a whole ruck of suited connectors..... not too many Aces in that range, and for this reason, I try not to be overly afraid of the Ace on the flop. In fact, if we are able to peg him as a good player, there should be very few Aces in his oop 3bet calling range)
That said though, if you have reason to believe is anything other than a good player, his range probably leans toward most Aces.