I've repaired quite a few stripped threads with helicoils, and I wouldn't hesitate to do it with it installed. Stuff a rag in the intake to keep stuff from falling into it and do the deed. I've even omitted the drilling and just used the helicoil tap when the threads were completely stripped away. It's not all that hard to run the tap in straight, as there's a pilot hole already there. And cast iron isn't that hard to tap, nearly as easy as aluminum.
I agree with bartamos though in that taking the manifold off would be the best (and safest) way to do it. It's not that much trouble to take it off, but it's not absolutely necessary.
