"If the problem code is really "1% or less of the code base", why not rewrite that code yourselves and then you can distribute the whole under whatever license you choose?"
We could do that, or even just do without the functionality provided by the outside GPL3 code. Still, even as our own project, a non-free relicensing to accomodate the App Store would make me feel like Faust making a pact with Mephistopheles (or perhaps Anakin exploring the dark side of the force, if you prefer).
It's more a balance between our young users saying "Cool! Tux Math is on the iPhone/iPad!" on the one hand, and on the other hand me and the other devs bemoaning the rise of an incredibly locked-down computer platform. I'd like to get our program on it, but only if we can do so under proper Free Software terms.