It's possible that they let him get that far on purpose, since it offers pretty irrefutable proof that he was attempting to flee to a foreign country. Also possible that there was discussion of letting him go, if Dubai and Pakistani officials could be pinned down on specific commitments to limit his movements afterwards.
Things were happening quickly, with a lot of agencies, both domestic and foreign, involved. It may be that they originally wanted to let him lead them to his associates, but then were able to determine who his associates were before the flight departed.
In the world of intelligence, things are rarely as they appear. For all we know, there may have been a dozen FBI, CIA, Dubai, Pakistani, and UAE intel operatives seated on that flight, all assigned to keep tabs on Mr. Shahzad.
I have pretty much the same scenario. It’s the told “let the auto thief get back in the car” routine.
It’s kind of interesting that they had ICE make the arrest, though. Maybe they just didn’t want to tip anybody.