Good points. I agree that this is altogether suspicious, but there's just not enough here to explain what was going on, let alone prove it. There is obviously much, much more to this story than this article presents. The quotes from named sources, like Vince Cannistraro and Paul Kurzberg's lawyers (semi-named) are helpful, but there are a lot of red flags, like copious quotes from anonymous sources, that demand circumspection.
If these guys actually were Israeli spies tasked with "launching an intelligence operation against radical Islamists in the area, particularly in the New Jersey-New York area", Israel must be running out of talent, because real Israeli agents tend to be pretty good at staying out of the limelight, would not be stupid enough to attract attention to themselves on 9/11 (an extraordinary feat of stupidity unto itself) and would sure as hell have had a better cover story or means of evasion if discovered. Also, these guys don't seem to have handled their arrests and detainment very professionally.
Whenever espionage is involved, it is often difficult for journalists to nail anything down. Sometimes unidentified "sources" are absolutely truthful, sometimes they are flat out lying, and sometimes they are made up by unscrupulous writers looking for a scoop.
I agree that common sense (as uncommon as it is) is a valuable tool for analysis, and definitely should be applied here. Common sense precludes jumping to conclusions based on speculation and innuendo, both of which are abundant in this article.
Hopefully, this 20/20 piece will cause more details to shake out, and perhaps some corroboration -- ideally the videotape -- might follow as well.
Imal