Well, if the ants ever start causing significant damage to humans due to this genetic similarity (attacking crops or even, in a more sci-fi spirit, attacking people), shouldn't it also help eradicate them more efficiently due to them being one large monoculture?
I guess, but I would think that they would have to create a lot of damage to make it cost effective to engineer something that would hit them at the genetic level (taking advantage of their genetic similarity).