1) I would tend to consider that as a mostly non issue to my opinion. Well, maybe I haven't had to face it proper and so on of course so take my view as an outsider view of things... I think that firstly, division doesn't happen only for tribal or fragmented societies like the Gallente. There is division in the Caldari, and there is division in the Amarr. True, they have unity under a bloc that is required, for the Amarr under their emperor, and for the Caldari, the trite "my corp against your corp, and the caldari together vs outsiders". Well it works too for the Minmatar: their tribes are rife with inter tribal conflict (but a lot less than inter caldari mega conflict in my opinion), but they are always united against the Amarrian threat. Secondly, I think it is properly silly to equate IC to OOC and bring those division on the OOC level. Players behind different tribes and minmatar characters can still talk to each other OOC like friends, and set up things together, much like it is done on the Amarr side (because believe me, between the witch hunts, calls for heresy, and all the oppressive side of the Amarr society, there is a truckload of conflict too).
2) I feel that there should be a difference between a minmatar only identified by his nemesis that suddenly becomes moot and less than nothing when you remove that nemesis (the Amarr slavers), and a minmatar identified by his tribe, his nation, culture, and customs, who has a common enemy: the Amarr. If you remove slavery and the Amarr of your background and everything related to your character, ask yourself the question "what is left?"... If there is nothing left, then there is a problem I think.