In Faraday's time, the paradox was not so much that there should be no EMF, but that there should be no flux if the magnet rotated with the disk. The resolution is that the magnetic field lines remain stationary even while the magnet rotates, so that the rate at which field lines cut across a line between the centre and the perimeter is not zero. It is really just for open wire segments that Faraday's law is derived, and we make use of it for closed loops in special situations. What is fundamental is the Lorentz force, $F = q \vec{v}\times \vec{B}$, or the existence of an electric field $\vec{E} = \vec{v}\times\vec{B}$ in the frame of reference in which the conductor is stationary. From these laws Faraday's law can be derived in certain situations.
Edit:
I suspect that you're after an answer that doesn't exist. Faraday's law is a mathematical statement that we try to make memorable by saying "the rate of change of flux through a loop is equal to the emf", which then loses a lot of what is actually going on.
Another person, Dims, gave the explanation of thinking of the disk as a limit of wheel spokes, and you were not satisfied with that answer. Instead, consider the case where the disk is continuous but the magnetic field only exists in say, the first quadrant. Now, pick a pizza-slice-shaped loop that is about to rotate across that quadrant. There will be an EMF around that loop according to Faraday's law. That is the statement that $\oint\!d\vec{r}\cdot \vec{E} \neq 0$ around the loop. This integral, I hope you can convince yourself, only depends on the radial parts of the path around the pizza slice, and not the circumferential part. This means that $\int_0^R\! dr \, E_r$ on one side of the loop is not equal in magnitude to that on the other side. I hope you can convince yourself that the EMF around the loop is solely due to the side that is entering the first quadrant, and not due to the part that is in zero field. Therefore, $\int_0^R\! dr \, E_r \neq 0$ as long as part of the slice remains outside of the first quadrant.
But that part of the slice contributes nothing to the integral, and might as well be lifted out of the plane of the disk, far away from the generator, in such a way that the flux is unchanged. You could imagine realizing this loop using electrical leads attached to your voltmeter. Therefore only the part of the loop that is in the magnetic field needs to be considered. That the result remains true for the entire disk follows from the principle of superposition.
Edit 2: If you don't want to talk about electric fields, you can simply say that the EMF around the closed loop is the sum of the EMFs due to each segment of the loop.