Should you fold the best possible hand?

The title of this post is slightly misleading and I'll get to that but stick with me. There are times in hold'em when it is correct to fold the best possible hand at the time. In Omaha there are plenty of possiblities where you can have the best possible hand after the flop and still be an underdog but it's fairly rare in hold'em for this to occur. One example I have comes from a hand I played a couple of months ago on PokerStars. I was playing in the $5/$10 no-limit game when I decided to limp in from the cut-off with A4 of hearts. 4 of us took the flop which came K J T with two hearts. This was a pretty big flop for me. I had 9 outs for the nut flush (maybe the J and T were hearts making a straight-flush possible I don't remember) and 3 queens for the nuts straight (not double-counting the Q of hearts). It was unlikely but not impossible that an ace may get the trick done for me also. I called a $25 bet from the big blind which put about $90 in the pot. My opponent and I both had begun the hand with about $1000. The turn brought an offsuit queen which gave me the nut straight and the nut flush draw. In other words, I was free-rolling my flush if I was up against another ace. My opponent bet out $70 at me and at this point I couldn't wait to get as much money as possible into the pot. I was praying that my opponent had an ace also. How much should I bet here? I didn't know much about my opponent but I hoped that he wouldn't fold an ace so I moved all in for about $895 more. Technically, my opponent can fold an ace here. It's a very close call though. If my opponent somehow knew I had an ace and a flush drawa than it is definitly the correct fold. You see, my opponent will lose the hand about 20% of the time and split the pot the other 80%. He will never win the whole pot. His expected value is therefore approximately 40%. The calculation is (20%*0 (you lose) + 80*.5 (you get half). He's being asked, though, to put $895 into what will be a $2020 pot. $895/$2020 is 44.3%. He should have an expected value of at least 44.3% if he's going to risk putting $895 into only a $2020 pot. The obvious argument against folding is that you can't be sure your opponent does have a flush draw here. Possibly your opponent has only the ace of hearts. Or, your opponent doesn't have a heart at all but doesn't think beyond the fact that he has 'the nuts!'. Oh yeah, in the actual hand my opponent called in a nanosecond. The river was the harmless 3c. I was a little confused but not at all disapointed when my opponent showed trip tens and I got the whole pot. Ship it!