I'd damn certain there would be inter-faction treaties forbidding the use of WMDs, and imposing heavy control over largescale terraformers. Also, the destruction of the Nakessh's planet was helped along by nuking nanobot infested areas.
On another note, I foresee good relations between those Nakessh who embrace nanotechnology and those H2.0 who don't spurn it (i.e., the great majority of them). Heck, the 'Type 3' Nakessh pretty much are H2.0, or perhaps more accurately N2.0.