Hopefully Bethesda would put in reasons that would make people more hesitant in supporting the rebels (which is unsurprising the popular choice) for the sake of grey/grey morality.
Personally I will be setting alight rebels with cleansing fire as makeshift torchs for my battlemage. Assuming that is if I'm forced to chose between the two rather then say stop the fighting at the moment to better fight Aduin which in my mind kinda takes priority.
Personally, I generally tend to side with rebels in these sorts of RPG scenarios.
However, since the Empire has generally been more welcoming of all the various races and sort of a melting pot, do you think the Rebels will likely be somewhat more racist, or contain a xenophobic, semi-racist sub-group?