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I'm looking for fluff of something similar to the IG - SM fight in DoW: Dark Crusade.

With both sides claiming to be loyal servants of the Emperor.

Probably on both sides of the badab war

Space marines & IG include all space marines, renegade and excommunicated.. So yeah they are continuously involved in battles. The whole IoM vs Choas plot line of 40k is just a glorified civil war really.

You should be looking for moments in the fluff history when space marine chapters switched over to the not so loyalist side, or when there was some other sort of rebellion uprising in the IoM. Badab war is a good one, but so is the horus herecy, Obscuran Uprising, Constantinus Iconoclasm and all lesser known battles.
This list is could be what you are looking for. -> http://wh40k.lexicanum.com/wiki/List_of_Anti-Imperial_Rebellions

In the series "Soul Drinkers" the Soul Drinkers are hunted by the entire imperium - I guess technically they are "heretics", but in reality they are as loyal as any of the chapters - they just have been slightly (and by slightly, I mean a lot!) tainted because of some old chaplain....

I can't recall if they face guard alone, but definitely there are guard along with mechanicum and other space marines (IIRC its the imperial fists...)