Janiven is used a couple of times to introduce other people, but her role can be easily replaced by Arael in all those cases (at least those that I can recall).
Having her be (or just be framed as) an agent of the Council is a pretty interesting development that could be a lot of fun as it opens a lot of possibilities. She could be actually associated with the Council, or she could be innocent (you mentioned the PCs framed her). If she was innocent and was framed, it would not take long for the Hellknights to figure it out (Discern Lies and all), and come after the PCs. Would make the campaign a lot more interesting to have the Hellknights be a major factor.
Janiven and Arael's roles can be made interchangably. How do I know? The PC's eccidentally got Arael killed in my game.
The primary purpose of Janiven/Arael is to say to the PCs, "Here is your next plot hook." As long as you feel comfortable keeping things rolling by your own devices then either or both are disposable.
Areal/Janiven and the rebels are a good starting base to get the ball rolling. Their first apperance gets the party together and points them in the right direction and the rebels offer a base and lots of RP for those that like it.
If you want the party to be more independent, have J/A suggest that they break into two groups, this lets the PCs go do things on their own while still offering the chance to do things with the rebels.