That is a very good question. When I first read that, my impression was that the marshal was unable to defend himself going toe to toe with Stowers. If we had more detailed information about the two mens build, that may have shed a little light on this subject.
It would appear that in the heat of the battle, the marshal may have felt that the only course of action was to subdue the attacker by shooting him. The article doesn't give us any indication that the marshal had a history of violent or irrational behavior in performing his duties.
I'm just drawing conclusions, as you are, from what I've read, and I don't wish to read into what transpired.
Yesterdays thread sheds a little light.
http://www.freerepublic.com/focus/f-news/1415239/posts
The part where he testified that he jumped out of the way then fired is pretty clear.