CONCORD just "turning off" all capsuleers would not be the most productive response at all, as it would drive capsuleers towards working with the pirate factions.
A far more realistic response would be to play the capsuleers against each other - to use some names from CCP's trailers, CONCORD would go something like "hey, Blackhawk alliance, you really don't like those Drekar alliance guys, right? Well, they did something we really don't like; for the next 72 hours they aren't going to be able to target anything. Here's the locations of twenty of their titan pilots and the passwords to the starbases they are parked in. Have fun!"
Assuming CONCORD did opt to engage in a direct confrontation with, I think people tend to underestimate how much control CONCORD and the Big 4 empires have over what the average capsuleer can do. They are capable of limiting what our sensors see, when and what we can target, even when and where we can jump. If CONCORD wants to lock you down as a capsuleer, they are entirely capable of doing so.