Preflop
If you isolate to like 4BB, he is probably never folding, and then you are out of position with A9 and 25% of your chips already in the middle. That does not sound like a profitable plan, so for me a small isolation raise is not an option here. You could jam over his limp, but with 16BB you are not getting the best risk-reward, and A9 is not exactly crushing even a limping range. When I make such plays, ICMizer usually hates them. So unless he was a total drooler limping like 80% of
hands, I do think, just completing is the best line here. Folding would be way to tight.
Flop
With this being a limped pot I prefer to lead out, when I connect with the board. And top pair certainly qualify as connecting. As played the check-jam is fine, although you could also just call and look to play some later streets.
Results
It seems like, you are still very focused on bad beats, which this hand basically is. Even to the point where you dont even realise, how much
equity the opponent actually had. He was not calling "on a draw that had to hit twice". He had a gutshot to broadway, which would be the nuts, and he also had a BDFD.
More importantly though poker is not a game of justice. These $1 SnGs on
pokerstars can be played with a long term ROI of at least 25%, and that is exactly because, there are people, who will stack off light, like this guy did. If they always lost, they would likely stop playing pretty fast. But because they are occationally rewarded by lady luck, they keep coming back and donating their money to the game a dollar at the time.