#Conclusion
I would allow both letting go of the polearm to punch, and punching with the polearm in hand. I would allow both cases to happen without requiring extra investment or enforcing additional penalties. Either maneuver is equivalent to attacking with armor spikes or a (non-punch) unarmed strike anyway, so there is no particular reason why this approach should be worse, to my mind.
I might object to punching with certain weapons in hand. For instance, a punching dagger stabs someone when you punch them: it’s hard to imagine an effective way to punch someone without stabbing them while you have a punch dagger on hand. Maybe an overhand smash, hitting with the bottom of your fist while the blade sticks out to the side, but that might be awkward. “Might be awkward” sounds like a reasonable place to put in a small attack penalty; probably just −1 though, since you can see how it would be done and it doesn’t really take fantastic skills to make it happen.
But punching with a polearm, or punching with a polearm in the other hand, doesn’t really seem awkward at all. Those I would just let happen.