I agree that none of these aircraft are flyable if their flight control systems are shut down - and I think that's where you're coming from. However, many of these aircraft comprise modular systems that can and are designed to work independently should the others fail (a proper fail-safe redundant system of systems), so any attack would have to be quite accurately targeted and delivered to bring a manned aircraft down. Indeed, such a feat might not be possible on a flight control system unless you can actually get your hands on a comm port (that's how I'd make it, anyhow). Designing the redundancy capabilities of other systems to cope when one fails is something I imagine the designers lose a lot of sleep over, especially when the number of possible failure modes could be huge...