The Reach was doing the metagene research for quite a while before they actually got invited onto the planet, is what I believe is the issue. That's the treaty-violating bit. Once they're invited in, they can do whatever they want.
But yeah, there is the Mars problem. They'll have to blow up Mars to cover up blowing up Earth.
... this is one of those plans that ends up with the sector on fire, everybody dead, and Black Beetle missing his hat.