That's really what it boils down to: how did her having sequentially-numbered checks endanger the flight? Did they think they would explode, or that she would use them to attack the flight attendants?
It's not quite that simple. If, in the course of security inspections, the TSA finds evidence of a crime not connected with security, they are authorized to detain that person and involve the local police. If, for example, they search a carry on and find a pound of cocaine, that person will not be cleared. The cocaine would not endanger the flight, but that would not matter. The police would be called to the screening area, and they would handle it from there. That, by the way, is one reason that Amtrak is so popular for moving drugs and why DEA agents sometimes show up on Amtrak. Taking cocaine or other illegal drugs on flights is not a wise thing to do.
Now, is having sequential checks written to two payees with one payee heading out of town with them sufficiently suspicious to have the TSA involve the police? I have no idea. Add in possible behavior issues. Add in lack of cooperation. Maybe then? I still don't know. But, is it absolutely not probable cause for police involvement? I can't say that either.
I am always skeptical of any "good vs. bad" articles like this, particularly when the article presents one side extensively and the other side minimally. I have had first-hand involvement with situations like this and with this particular newspaper. You can give the newspaper tons of information, lots of facts, and if it doesn't fit the point they are trying to make, your side is reduced to a sentence or two, and the readers think you did not offer any information and conclude that you had nothing to offer. You're lucky if they even spell your name correctly.
Knowing what I know about TSA and TSA procedures, I am skeptical about this tale of woe.