Because suns are big and shiny? Oooh, shiny...
Laforge's method of destroying the alien "gun ship" was dependant on a bit of stupidity.
The Gun ship could have easily paced the Enterprise at a higher altitude, remaining in vacuum, while the Enterprise plowed through the atmostphere. This would have also presented the gun ship with the best firing aspect on the Enterprise, from directly above.
(Be kind of hard to miss)
Except that one thing the atmospheres of inhabited planets do very well -- without which none of us would be here -- is absorbing or scattering radiation. Although the writers of TV and movies tend to overlook it, air is made of stuff. If there's a large enough quantity of that stuff between you and whatever's shooting energy at you, then that stuff is going to absorb most of the energy. Sure, Trek's given us plenty of episodes where a ship fires phasers from orbit and destroys something on the ground, because TV writers don't understand science. But even if you assume that phasers are tuned to some frequency window that lets them avoid absorption by the atmosphere, that doesn't mean that every kind of weapon could do the same.
So if the probe didn't have the right kind of weapons, then the deeper the ship got in the atmosphere, the better shielded it would be from the probe's weapons. Which would give the probe a reason to pursue it and stay close enough for the weapons to retain their full effect.