I doubt they will do this but who would like to see sub factions have mini-wars against themselves.
Lets face it Dark Angels and Space wolves will never get along,

If they wouldn't include it in the game somehow i don't think Ivan would have asked us what kind of Rivalries we would like to see.
http://forum.eternalcrusade.com/threads/classic-warhammer-40000-rivalries.30117/

Ok he might have meant loyal against chaos and like that but a lot of people mention rivalry between loyal and loyal, chaos and chaos. So hopefuly Space wolves could swear at the stupid Dark angels blocking our path of fire.

It's not heresy to persecute traitors.... Sorry I meant Dark Angels

Mini-wars in the same faction? I don't think so, at least not for Imperial Marines and Eldar.
Sure, some chapters, like the mentioned Space Wolves and Dark Angels, may have ancient feuds going on, but they don't murder each other in small wars like they're fighting heretics.
The most we should see is non-lethal duels in friendly territory, like what we see in other MMOs when players in the same faction can start duels.

Wait until the Minotaur's are introduced, who will actively murder other loyalists and steal all their stuff with a nice "HIGHLORDS OF TERRA APPROVED." stamp.

For the Dark Angels and Space Wolves its not uncommon for them to have a chosen champion (from each chapter respectively) have an honor dual of sorts to keep the truth brotherly rivalry the Lion and Wolf King had during the Great Crusade alive and strengthen ties of kinship.

this could easily be worked into the game not just for imperial factions but chaos eldar and orks with, 'training/ sparing rings' for solo combat or group tactics were death is not the outcome but no exp is gained, along the lines of fun social fights.

There should be elements in the game that play on interfaction rivalries. I dont think we will see a Black Legion raid on a Word Bearer base seeing as how they will all have the same bases. If we saw sub faction objectives that while not harming the other sub faction give your sub faction an exclusive bonus it would fit with the idea that even in a joint operation between allies, you are trying to bring honor to your chapter.

I see no problem with this. I think most astartes doesn't really care about what happened many years ago between Dark Angels and Space Wolves.
Ofc there are some fights here and there, but in the end, they will fight along side each other, not against each other. Like brothers.