I just looked through my 3rdR rules and this situation is not covered. But given the fact the ship being tractored has engines and can resist the movement means it is unlikely to allow itself to be tractored through the planets atmosphere, even if pulled into the same hex as the planet. The planet occupies only a small fraction of the hex. For the ship to enter the atmosphere would require the tractored vessel cooperate.
A PDC tractoring a ship would cause a ram attack to occur if it attempted to pull the ship into the atmosphere. I believe SM2 has some rules covering this (I didn't see specific rules covering ramming PDC in 3rdR but I might have missed them...I'm fairly sure they are in SM2), if not the UTM probably does.
So long as the enemy ship can resist movment (all bases can do this, and any ship with at least one operational engine room as well) then I would say it is impossible to do it. It could be done to a ship without engines or whose engines were for what ever reason inactive (totally, even on station keeping the ship can manuever to miss the planet).
That would be my interpretation of the rules.