I really don't see why the intra-Crusade rivalries are such a deal-breaker. "Allies" have been betraying and fighting each other for millennia now. Peucestas sold out Eumenes by holding his cavalry back at the battle of Gabiene. Julius Caesar fought his erstwhile ally, Pompey, and then Octavian and Mark Anthony played a game of alliance-and-betrayal. Countless soldiers died as a result of such rivalries and duplicities, often without ever knowing the reason why.
This wasn't simply a case of the Jantine Patricians being jerks to the blue-collar Tanith. Hechtor Dravere, their patron for some time, wanted to become Warmaster and take over the Sabbat Crusade. Drake Flense wanted to avenge his father. Ibram Gaunt was their mutual enemy, and the Tanith First-and-Only were in their way.
The bit with the Volpone "Bluebloods" is, admittedly, more awkward. General Notches Sturm never really gives a better reason for wanting to wipe out the Ghosts other than they are an embarrassment to the current Warmaster, Macaroth... but we later find out that the Volpone can be a somewhat imbalanced lot (see the Sabbat Crusade anthology)... so who knows what was going on behind the scenes.