Garbage Disposal / Plumbing Dilemma
Anything could be possible. The benefit of the wye, the way it is setup, is for cleaning. If you don't forsee any future problems with cleaning, I would cut it out, and use a threaded set of pipes. This way you can still remove the pipes if you need to clean it out and if you need to make any adjustments to the drain, this will make it easier to do. Once you figure out the height needed for the disposal, you can re-plumb the drain. But make sure you still have room for your p-trap setup.

Also, is this a single sink or a double? Perhaps if a double sink, have you thought about reversing the drain and disposal setup?