The immobilizer system can not lock you out of the other modules, your scanner should be able to communicate with the PCM regardless.
I'll admit to being completely unfamiliar with the Snap-On scanner. I work at a dealer, and we have the factory scan tools.
It happened when you stepped on the brake, all that really does is turn the remote start off, but as far as the car itself is concerend nothing changes (as the circuits are still powered up by the ignition key) so the car doesn't even look at the key. (it's only checked at startup).
If it somehow managed to blow the ignition fuse under the hood the car won't start, but you've checked all the fuses and I'm assuming they are good.
The only other issue I can think of is if it somehow was connected to the PCM wire on the
At this stage, here is how I would go about trying to get to the bottom of this issue...
1) I'd find a similar car and see if the scanner is capable of talking to it.
2) Unplug the PCM.. see if you can access any other modules (abs or airbag). If you can the PCM has issues that are preventing the car from starting and effecting the data bus.
I think you have PCM issues, you should hear that fuel pump coming on for a 3 second prime when the key is turned to run regardless of data bus or security status..
If you unplug the pcm and still can't talk to anything, we'll have to get into vehicle communication, a tough job online like this, but I'll give it a shot.
Give 1+2 a try, and let me know the results and we'll take it from there. I have to post this as an answer, but please don't accept until we come up with a resolution!