Folding the nuts?

[Guernica4000]

I need a little help with this hand. I am sure I miss played it but I need to know if I am realizing the error because I am being result orientated or if my math, the chip stacks and the timing supports my later analyzes of the hand.

Multi-table tournament with 300 players left the first payout is 100 players away.
Blinds are 100-200
Chip leader (approximated) = 20,000 tournament
Chip leader table Hero with 12,540
Avg. stack tournament= 3,500

Here is the hand:

Villain has 11,800 and is in MP it is folded to him and he bets 400.
Hero is button with A [img]/images/graemlins/spade.gif[/img] K [img]/images/graemlins/diamond.gif[/img] folded to hero, Hero bets 1,000.
Blinds fold Villain calls. It is heads up.

Flop is
T [img]/images/graemlins/diamond.gif[/img] J [img]/images/graemlins/heart.gif[/img] Q [img]/images/graemlins/club.gif[/img]

Villain checks, Hero bets 1,000 villain calls.

Turn is K [img]/images/graemlins/club.gif[/img]

Villain goes all-in hero calls.

River is 7 [img]/images/graemlins/club.gif[/img]

Villain wins hand with A [img]/images/graemlins/club.gif[/img] 8 [img]/images/graemlins/club.gif[/img] Flush

So after losing the tournament I analyzed this hand and I think I should have folded. Here is why:

I was 99.9% sure Villain had the Ace I had been playing with him for about an hour and there was no way in my mind he would bluff or semi-bluff there.

So if I call I win 1/2 the pot or $2,150 3 out of 4 times but if he is on a flush draw and hits I lose 11,800 1 out of 4 times. Now I don't know how to calculate the probability that he is on a flush draw so I need help there.

Second reason to fold is that if I fold I still have 10,000 chips and a chance to win the tournament or at least finish in the money. If I call and win I have 12,700 but if I call and lose I can get crippled needing to get very lucky to come back.

Comments please. Should I have foleded? Why? Why not? Thanks