Sometimes Rambaldi can get in the way. But Rambaldi's been a part of Alias since the beginning. The Rambaldi stuff is important to the storyline. I think that I'd be fine with subtle Rambaldi overtones to the show. It doesn't appear that there are really any objects to go after anymore so that leaves the prophecy (and the possible reappearance of the Sphere of Life). Besides, I don't think anything else could turn Sloane evil again except Rambaldi so we need him.
Rambaldi makes things interested. There is always something new and unexpected going on when you're dealing with Rambaldi. and they never really closed that chapter of Rambaldi at the end of s3, did they?