Well I'm not sure exactly how the Grand Cannon (or the Macross operates) but its basic science that even being destroyed by them would just convert the mass of everything into another form (vapor, constituent molecules, etc)... which could be worse than debris that can be dealt with (pushed into the sun or out into space or on another, lifeless, planet/moon, etc).
Do we really KNOW there were "thousands" of impacts from Zentraedi ships on the surface of the Earth? Why? I don't seem to remember lots of kamikazes on the ground bombarded surface (that wasn't that thorough it looks like...)
Good thing that South Ataria island happened to be where the ASS landed.
It's logical that there were thousands of impacts. You don't just destroy 1.8 million ships and not have debris, even if most if it's sent flying out of the system(my assumptions regarding the Grand Cannon involved imparted velocity from the beam impact to the vessels/debris/vapor).
What we KNOW is that ...
approximately 1.8 million Zentradi vessels were destroyed in Earth orbit;
one battleship, one fighter pod(Quel-Quallie, I think's the right name), and one GERWALK crashed on the surface;
all 3 were largely intact;
the battleship and fighter pod both imbedded themselves well enough to stand vertically while all 3 hit lightly enough to not destroy themselves;
and the surviving humans began an atmospheric purification operation within a month of victory.