Yeah, after Disney bought Marvel in '09, they didn't want to wait until the Paramount distribution deal expired, so they bought Paramount out of Avengers and Iron Man 3 (Paramount still handled Iron Man 2, Thor and Captain America). But yes, as Akwat Kbrana said, part of the deal included the Paramount logo showing up anyway. If I remember correctly, the Marvel logo actually appears before the Paramount logo at the start of The Avengers.
I'm assuming Iron Man 3 is all that's leftover from the Paramount deal. I can't imagine a Disney logo showing up in the trailer for Thor 2. It'll probably just be the Marvel Studios logo and that's all, same for the start of the movie itself.
Likewise, I can't imagine a Disney logo showing up in front of Episode VII. If they distribute, I would think we'd open with the Lucasfilm logo and go straight into "a long time ago in a galaxy far, far away."
Oh, and as for the whole Fox thing, I think it's totally possible since Disney's not gonna want to wait until 2020 to get their hands on Episodes I-VI. They're gonna have to cut a deal to get Episode IV anyway, since Fox owns those rights in perpetuity. When you consider all of this, that percentage really does seem quite small. It would be worth it for Disney to give Fox theatrical rights in exchange for the six existing films.
It's worth noting that we still haven't seen a 3D blu-ray release of TPM. Perhaps this Disney deal was already in the works behind closed doors way back in February and that's the reason why (but who knows).
If I had my way, I'd somehow make sure that any future "Episodes" had the Fox fanfare at the beginning. Who is to say Disney-Lucasfilm won't want to eventually do X, XI and XII (or even XIII, XIV and XV)?