This, of course, breaks the known laws of physics, since lightspeed is a hard limit on the speed of causality. You can't use entanglement that way in the real world (if QM is anywhere close to correct)
But accelerating them towards earth “at the speed of light” isn’t exactly a problem. The LHC accelerates protons to about 3 m/s less than the speed of light, and as far as the plot is concerned the sophons travelling here at the speed of light, or some tiny fraction of a percent less than the speed of light doesn’t make any difference.
The aliens had instantaneous communications, and could directly influence events on earth, but still had to travel at sublight speeds? It wanted at least an acknowledgement of the inconsistency, and a token effort at explanation. As others have noted, it’s not at all clear why they couldn’t simply have killed off the humans remotely.
As already said, that preserves the planet, prevents a potential enemy from further developing technologically, and enables real-time monitoring of and interference with that enemy's activities.