If you are a Manderly, a Reed, a Mormont, or an Umber (by the way, is the Greatjon dead or imprisoned?) would you rather be ruled by the Boltons, the Baratheons, the Greyjoys, or the Lannisters? Those appear to be their choices at the moment.
Of course, they could choose to fight against any non-Starks. But this seems problematic at the moment. One minor northern house standing alone against Stannis, Euron, or Tommen/Roose seems like suicide.
It appears that Mors Umber at least is willing to back the Boltons. For the Umbers this seems like a no brainer... With the Starks in charge, the Umbers are behind the Manderlys, the Karstarks, the Boltons, and possibly the Hornwoods, the Cerwyns, the Glovers, the Reeds, and the Mormonts as well. By supporting House Bolton, House Umber moves up the ladder.
As to the original post... I think one of Martin's themes is might makes right. Not right in a moral sense, but certainly in political terms. The Children of the Forest were beaten by the First Men. The First Men were beaten by the Andals. The Rhoynar successfully sliced themselves a piece of the Westerosi pie. The Ironmen of the Iron Islands certainly live by the idea of might makes right. Aegon the Conqueror subdued the Andals, the Ironmen, and the First Men. Robert was not the true heir of Aerys II, but he became king anyway. If you are the strongest, you make the rules. No more, no less.
If Dany finds out that R+L=illegitimateJ, she could legitimize Jon. Or she might decide to kill the whoreson anyway.
