1. Under E, it is says that isolated marbles are not compulsory to be captured.. do the marbles then go to the pool?
I think this is just an unfortunate phrasing. If you isolate a group of marbles that have no empty spaces, the player that created the situation must take them. What I think they are trying to say is that creating these situations is not the only way to capture marbles.
2. Under E, number 2 doesn't make sense to me. If you isolate a group with 2 empty spots and 2 marbles, what happens?
Nothing. The game keeps going. The board does not have to remain connected.
3. Is the isolated group the group with less spaces? In other words, could you theoretically split a group evenly in 2?
It doesn't really matter if they both have free spaces. If one (or both) have no free spaces, you capture all of the marbles in the group(s).