Well, a there are stealth scripts that can be found in the AUM's. Not sure how good they are, but it does not sound like a hard thing to code.

Alerting guards, this could be done using the viewing "cones" and distance (also in the AUM's). Again, not sure if the code in the AUM will be exactly what you want.

As for the putting your back to walls, have never seen it done.

I once thought about making something like this. Not necessairly a clone of MGS, but the same type of game. The project never got started because I didnt know how to do a lot of the things I needed to do...

Anyways, good luck.
Raddaddy