I doubt you would describe what was done to River Tam as "agents of order".
No, of course not. But neither do I think the entire Alliance was in on that. Some super secret black ops organization, possibly unknown to (or even forbidden by) the Alliance proper. Kind of like their version of Section 31.
Of course, I am trying to put the best positive spin on this. It's what I do.
Plus, you gotta love those Alliance ships...