Detonating over Severnaya ensures that only they have control of the 2nd satellite.
If it had been left intact, the military would be able to use it to change codes and lock them out at will, possibly even without the launch keys. After the initial heist, there's no way Russia could rebuild the facility from the EMP blast in time to prevent a second detonation. It also covers the general's role, so it's a twofer.
Speculating on this bit, but there may also be a matter of timing. They were able to task the sat, target, and detonate over the base in the time it took them to leave. If they tried for London right off the bat, the weapon may have taken way too long to get into position, leaving them to greet the incoming army with more guns. The general's "inspection" may have been timed for precisely that reason; he would know when the weapon would be overhead. They would also need to time the heist out of London to their spec - too much time between theft and detonation and people would know what they'd done, too little time between detonations and it looks too much like an inside job rather than an outside theft. The way they do it lets everyone get covered.