As the title states, Do you think ZMS would allow us to make a choice between reclaiming your soul being a loyal servant to him.

The four corners of the house of troubles aren't exactly known for being nice guys. The more likely outcome of faithfully serving Molag Bal would be that he turns you into a Lich. Or maybe a vampire.

same as in every TES game:
you won't be able to join the dark side

I did read somewhere that ESO should have real meaningful choices between good and bad in quests and so on, but I doubt that choice will be present in the main quest.

No, the main quest will be one-tracked towards bringing Molag Bal's scheme to an end.

Would be very cool if you could go either way right from the get go...you wake up in jail in coldharbour, Molag Bal or his minions attempt to get you to join them and when offered the choice you can go either way and play a completely different game ..it would make taking over the Imperial City more challenging with real players there to defend on Molag Bal's side.

It can be done in future to make faction alliance, and enemy faction

Yet, i hope not. It is not possible to balance 2 factions.
3 is fine

Does a plan to help protect the anchors in Cyrodiil from other factions count?