My bad, when I said seals, I meant guild marks of course. And no, they haven't taken out guild marks from the game. I'm looking at them in my inventory right now. We just can't do anything with them right now. It is still yet to be seen whether or not they will eventually have a purpose, or if we will be able to turn them in for gil/seals later.

As far as I'm aware, Yoshi hasn't decided yet. Even in the game the Guild stores say they are TEMPORARILY closed for business.