The problem is you think the Jets "had to pass", which I disagree with. By using the timeout at that point, the Colts guaranteed they would not have any time left to get the ball back, assuming the Jets know how to manage the clock. A 50-yard FG is risky, but they had sucess running the ball all day against the Colts. So maybe you try passing once on 2nd down (but not necessarily), and then run it on 3rd down, forcing the clock all the way down to nothing before trying the kick since the Colts now have no timeouts left. You're almost guaranteed you're kicking from less than 50 yards, and in those conditions the chances are decent.
If they don't use the timeout, it forces the Jets to move more quickly, maybe not get off the play the want, and perhaps increase the likelihood of an incomplete pass. Problem is, the Jets had 2nd and 3rd down to play with, so the most the Colts get, even by saving the timeout for later, is maybe 15-19 seconds.
It's a moot point to argue, IMO, because I think the Jets still make the FG either way. But to say that calling the timeout there makes sense to save seconds on the clock for later on is just not right.