"The US Army has to have zero tolerance. He should have been gone."

What should have been do about it?
Removing him from the Army would have just taken the problem off their hands and possibly made it worse. He would have mostly gone to the civilian sphere (see my former response)

You can't jail him for his beliefs unless we want to revive the Espionage and Sedition Acts of WWI

Complaining about it (mainly because he is Muslim) dredges up the flying imams accusations of profiling.

That's the problem with lone gunmen. How do you stop such future crimes without impinging on (or give them the ability to sue for impinging) rights

Is there a clause in the military or civilian law that can withhold someone (ie jail) for suspicion of future acts? Can we send lone gunmen to jail under attempted murder if we have clear evidence of planning for such an act? And what would be the criteria? Could it be watertight under defense accusations?

And as much as I like Lieberman, I think what he's doing is useless UNLESS they come up with a plan to protect military and civilians from such lone gunmen. Otherwise, L. is doing nothing more than a public censure

Red flags mean squat if there is no rules for follow up. It's a balance of keeping the rules strict yet generic enough so that discrimination arguments become moot.