Security system

You likely damaged the actual pass-lock sensor in the ignition switch. It has an anti-tamper function in it that will lock out the ignition if damaged. If it is cranking but the security light is on that is very likely the problem.

The switch is under the lower steering column cover. The key has to be in run for the switch to disengage without breaking the anti-tamper pin again. Remove the cover, turn the key to run, remove the screws and the switch. Reverse the process to install the new one.

Relearn without a scan tool. (Have had to do this two to three times on some vehicles before it seemed to actually work.)

Turn "on the ignition, with the engine "off".
Attempt to start the engine, then release the key to "on". The vehicle will not start.
Observe the security telltale. After approximately ten minutes, the telltale will turn "off".
Turn "off" the ignition, and wait five seconds.
Repeat steps 1-4 two more times for a total of three cycles/thirty minutes. The vehicle is now ready to relearn the Pass-lock(TM) Sensor Data Code and/or passwords on the next ignition switch transition from off to crank.
Start the engine. The vehicle has now learned the Passlock Sensor Data Code.

Important: The vehicle learns the Pass-lock Sensor Data Code and/or password on the next ignition switch transition from off to crank. You must turn the ignition off before attempting to start the vehicle.

Correct. Unless you got a key cut for the lock. Personally I tend to get the cylinders out of a yard then re-key them to fit the original key for the car. That way you do not end up with two keys and the potential for cylinder damage if you put in the "wrong" key without noticing.