Yeah, the thing about hypersonics is atmospheric density. There's a great reason the SR-71 flew at 90,000 feet+, the air's thin enough that Mach 3.5 was only heating the skin to 450oF or so. If you tried to do that at low altitude, you'd incinerate your missile like a meteor. Hell, some modern combat aircraft still can't break supersonic at sea level, despite being happily able to up at altitude. Once that hypersonic projectile descends to low altitude on its way to a target, it's going to slow down.
You're basically dealing with a ballistic missile, coming from rather high altitude, with both a radar signature and one hell of a heat signature. That's going to be plenty of warning to deal with things, and start lobbing missiles back at it - like I said, even your short-range Sea Sparrows from a RAM launcher accelerate to Mach 3.5, so dealing with incoming isn't impossible. A little more difficult, sure, and they can be fired from further back and have longer ranges to engage targets within, but unless they're shooting gigawatt laser beams from 100,000 feet they're not unstoppable.