That, by itself, still makes no sense. I did read somewhere that they're essentially treated as a Liberty Criminal/Terrorist Organization, and that Pirates like them.
That may be how their relations are at the very start of the Storyline, but at the end, the President knows who the Order are and is very thankful for their actions, even if such will never be public knowledge. The Order, by all rights, should consider nobody but Nomads as their enemies. Their ideals forbid them to consider any part of the colonies as their enemies. The only true enemy to them is anything that could jeopardize the peace of the colonies. Being at odds with the Liberty authorities would put them against that very peace they stand for.
And, I quote, "Do not interfere! We're here to protect the President! Schultzky's a traitor!"
Currently: Remastering Kiith Somtaaw's Acolyte Fighter. These Homeworld ships need some Sirius work done on them. ^.-
"Do not interfere! We're here to protect the President! Schultzky's a traitor!"
For peace throughout the colonies! We will never forget..
"He who controls the [insert orange powder drug here] controls the universe!"