I've been reading the posts between you and Hoichi, and I think you both are making valid points.
I do, however, think Domestic Terrorism should not be used in this situation. Here is why - there are plenty of other charges this militia can be brought up on that have hefty sentences. Criminal Trespass and Destruction of Federal Property (they tore down a fence).
If this militia were making threats, blowing things up, killing people, or harassing through menace (like the KKK) then I could see how a domestic terrorism charge can be brought up.
The wikipedia definition of domestic terrorism is as follows:
While taking over a Federal Building with an armed group may be considered an act of attempting to influence the policy of a government by intimidation - they have made no direct threats. They are not kidnapping anyone, causing mass destruction, or assassinating anyone.
I think that the Sheriff should give those who have shown up a chance to peacefully leave, and charge the ring leaders with conspiracy.