Well there must still be some Empire left, how else do you explain the civil war in Skyrim?
I didn't say the Empire was gone... just that it was crumbling, which it is.
There's not much left of it. So East Empire Company would probably be one of the first things to go away.
And the civil war is about the king getting murdered, and lots of tension between different high families. How the Empire is crumbling just adds on to that. At least that's how I interpret it.
Still, similar quests to theirs could be given to other people/factions, so there's no loss really