no fear of stupid aliens
I would hope that any species capable of figuring out the technology/science behind travelling millions of miles, millions of light years to come to our planet would also be equally as capable of having mastered solar/neutrino-powered self-replicating nanotechnology to such a degree that they can use our planet's primary power-sources (the sun, neutrinos, radioactive decay from our core, simple background radiation) to supply them the energy necessary to break our planet's materials down to their base properties (protons, neutrons, electrons, quarks-even further down if so their science prove this to be the case) and recombine them in anyway they see fit to do so. Such that, they can not only change our atmosphere and/or our planet into any shape form or function that they desire, but also do so in such a way that whatever condition they may come to said planet (ours in this case) and find it in, any readjustment from that base condition is seen as a mere inconvenience, and not one worth of intervening on previous to this terraforming.
Basically, I think we aren't even comparable to an 'ant hill in africa' to butcher the line from the movie Contact. Thus, no sleep lost here.