It's definitely going to change the dynamic in a major way. Assuming he's actually dead and not a vegetable. Well, I guess either way they won't be calling Bobby for help with research or to cover for them with the local police as their "FBI boss".
I actually think the leads are strong enough to carry the show on their own, and losing figures like that is a keystone of the show, but they're going to have to start introducing new people to kill off later at some point.
Oh hey, what about Bobby's budding relationship with the sheriff lady? Damn it, Bobby just has no luck.