It's the preponderance of the multiple factors (as cited in the article), along with the immediacy of the flight and the USG's well-documented predilection for pulling similar shenanigans for the sake of far lesser targets, that are sufficient to raise reasonable suspicion.

And it's the immediate dispatch of the plane which strongly suggests that the U.S. wasn't going to wait to go through normal judicial channels to pick up their target.

I would expect the US to have planned for how to perform such a kidnapping, because dealing with rogue agents in one way or another is very definitely someone's job. I would be amazed if there wasn't a report giving a number of options and pros and cons for each compiled—of course, how it was acted on is anyone's guess.