Of course aliens could do that, but would they? The evidence so far says that humans in possession of a superweapon, at least, don't annihilate one another simply because of the possible threat of superweapon acquisition posed by the other - otherwise we would have annihilated the Russians and/or Chinese in the 40s and early 50s.

At any rate one would think that aliens would at least understand the concept of mutually assured destruction and realize that we would not destroy them if they were capable of retaliating in kind...