Drop a super virus on us or irradiate the whole planet. Any species capable of disrupting our particle accelerators is more than capable of wiping us from existence.
In the book, they were scared of humanity's technological growth rate. They were observing our technological advances and noticed that it was significantly faster than theirs. While they were, at the time, technologically superior, they were afraid that after the 250+ years it would take for them to get to Earth, humanity would have become technologically superior; too strong for them to overtake.
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.
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.
If you need to wipe out the inhabitants but leave everything else so you can now use it, you need to not destroy everything in the first place. Otherwise, you now have to terraform a planet that you chose because you didn't need to terraform it.