From a gameplay view that could very well break the game, but if you don't ally... say the sisters of battle or the imperials with the space marines then you are a heretic and are breaking 40k lore. Only solution I could see to this is if we had another planet with imperials or sisters on one and space marines on the other.

Well. They said a couple of times that they wish to add every faction in EC (with time ofc). So I kinda wonder as well, what they have in mind.
That said, it's too early to be concerned with IG or Sisters of Battle (or any other faction, which is not on a list). I don't think we'll see 5th faction at launch.

Actually there are several occasions that SM's and other Imperial organizations didn't play nice with each other...Space Wolves and Inquisition comes to mind instantly...lore is made in a way that under certain conditions everyone can fight everyone.

IG and Sisters of Battle could as easily be one faction on their own, fighting against SM's, because they may have a very different agenda...

As it has already been stated it's actually not uncommon for Imperial factions to fight one another if their interest conflict with each other.
But you also have to remember that it's possible for factions to form alliances with each other.
The war council of a faction can invite another war council from another faction to a council meeting which takes place in the warcouncil room, which is in purely technical terms, an instanced room where only council members have access.

correction.
its uncommon for imperial factions.

that does NOT mean is doesn't happen all the time. but more often than not, they are working together.

If you have Sister of battle and grey knights just say they are trying to get the sisters blood to protect them from possession even though they can't be possessed it worked for Ward.

Some Marine Chapters have been known to shell, then assault Chaos forces that are in close combat with Imperial Guard with the SM not caring whether they killed IG as long as the enemy died, even in melee.

Each of the classic Imperial Factions has their own individual command structure which doesn't normally meet until it reaches the Lords of Terra.

Some factions will compete for a prize, like a piece of STC Technology or Archaeotech. Even honour and glory can lead to competition.

Some factions have rivalries and grudges, though usually at a low-level, with other factions.

Then there are the times when a bureaucratic error can set factions on a collision course which ends in combat.

Whether it's disdain, incompetence, grudges, or greed, even outside manipulation, there are easily a thousand and one reasons for different Imperial Factions to end up fighting each other.

I would hope they aren't perma locked. It would take away from potential "story" options over the life of the game, plus the Space Marines already have the biggest portion of players, the game doesn't need a Superfaction that nobody else can beat due to sheer numbers. That game would fail.

I'd like to see Dark Eldar.
If Space Marines are such a high population I'm seriously considering going Ork already.
We need more baddies not Imperial friends.

Or Tau. Most people like to play the Good Guys, and people are going to make the mistake that the Imperium are the good guys of this universe(when nobody is) but the Tau will draw from the same pool of new gamers and I believe even the populations the best.

Dark Eldar will just split the Eldar population in half. It's better as a second or third added faction.