They can't form their own order because they are directly under ONI control, I believe. Since the UNSC used the war against the Covenant to lobby for complete control of the government, I'd imagine development on the Spartan program would continue despite legal and ethical ramifications.
The UNSC Command and ONI aren't exactly made up of men and women of high moral standard.
[Edited on 02.17.2011 12:21 PM PST]