Visually the cockpit of a fighter plane is located forward, thus very likely ahead of the plane's CG. Ejecting the pilot would thus move the CG towards the back of the plane, which is a less stable configuration making it more difficult to recover from a stall.
A developed spin is an equilibrium of forces. Anything that disrupts that equilibrium has a decent chance of disrupting the spin, and that would include moving the CG aft.
However, see my other note as well, there would be a nose down moment when the seat fires. There would also be a massive drag profile change. Any of these things have good potential to disrupt a stabilized spin.
My main point is that it's almost certainly not the case that the pilot was actively making incorrect inputs before ejecting. The ejection itself is the variable that likely would disrupt a spin in such a situation, not the pilot no longer making inputs.
