This pretty much never happens. Either there was a bug or it was a really edge case.
Sometimes it's easier to do all of those things while the region is rogue, though, because I think that some of the daily penalties only apply when it is under your command.
That said, one region realms with 5 nobles is more problematic than 8k CS of militia... It's not the game's fault if you are too small to be viable. 8kCS is unusual for peasant militias, but it's not a very impressive force. A realm that is unable to muster at least 10k CS of mobile army isn't likely to ever be able to accomplish anything worthwhile.
