/speculation on
I doubt there will be a gray area where you have access to everything on both sides. After all, why be a hero or a villain and restrict yourself when you could be gray and have it all. Chances are at any given time you will be a hero or a villain, with maybe some transitional content. Realistically though, if you think of it, being gray would mean you are likely mistrusted by both sides, not trusted. So if there is some transitional spot where you are "gray", I doubt you'll have full access to either of the two sides.
As for grouping, I would guess that only the mission holder's morality would be affected to prevent people from changing against their will. If not, there likely or should be some kind of warning so players ahead of time will know in advance how they will be affected.
As far as supergroups, I would not be surprised to see this extended. As supergroups are a basis for the games social structure, I would not surprised if it would either allow both heroes and villains and work as they do now, or the same SG would be split so that the in game functional parts (like bases) are separated but still have a common communication system. I doubt that they will forcefully break you apart from your SG and friends just because you want to switch sides.
If there is any method to switch sides in Paragon/Rogue Isles, it will likely be limited (one story arc or such). What is more likely though is a contact in each side that sends you to someone in Praetoria to get you started.
/speculation off
Overall I have to admit, I'm excited about this. Usually with paid expansions comes a lot of new content. The free content updates are great, but every now and then you just need more than what can be otherwise provided.