You're making hacking it out to be some kind of huge complicated problem.
All you have to do, really, is get into his firecontrol or targeting or IFF coding and turn it from something that makes sense into a bunch of zeros. You don't have to do something fancy. You just have to render it inoperable. Hell, you don't even have to get all of it. Just a small bit. It doesn't take much to bring a huge, complicated bit of code crashing down like some kind of concrete slab house of cards. If you don't believe that, consider how simple it is to bring your PC to a grinding halt. Change one character in the correct place, and there are a lot of places to do it, and you'll never get the thing to work again. An AI of the type you propose would be vastly larger and more complex and have vastly more in the way of weak points because of it.
Put simply, because of its vunerablity to sabotage, such a construct would never be accepted for military service in large numbers. It can't be made secure enough. In relatively small numbers, perhaps, and hence with easily controlled physical access to them, but even then the cost of creating and deploying something like this against the cost of a human pilot wouldn't be very favorable.
