You can rush and if you take Minas Morgul and the Black Gate, Mordor is pretty much done for as their two main unit producing centers are gone (and you get two citadels).
The other possibility is as someone else earlier stated, if you kill all the family members the faction just dies. This has happened to me numerous times before, in both vanilla M2TW, Kingdoms, SS 6.1, and TATW. A faction with a huge number of cities just dies and all their settlements become rebel.
So in all reality it is very possible this happened, although in 1.4 this issue will be fixed
