If you push all-in here, the BB is going to call with any two cards because of the good pot odds
he is getting (call 2000 to win 5000 or 5:2 odds), so be prepared for a showdown. If you win this pot you will have 7000 chips. You most likely will get at least 8th place.
If the difference between 8th and 9th place is $500 I would imagine the difference between 8th and 7th is ~$750.
If I am in this tournament I push and either pick up the BB and have 5000 in chips or take my chances with the AQ and try to double up to 7000 to give myself a better shot to move up the pay ladder.
If you fold here, you are basically telling the table that you are going to try and settle for 8th place, I take the risk here and put my chips into the pot with a good hand instead of waiting for another player to get knocked out and having only 2500 chips.
You want to win the tournament if possible and folding AQ in the SB with no one else in the pot except the BB is a bad strategy to do that.
You are already in the money, you might as well try and maximize your profits and if you take a bad bet with the AQ, big deal, you still cash and in the long run you will make money on that play.