I have tried to overwrite my stock system about 3 different times, with no luck. I get stuck in safestrap, every time, and had to fastboot it every time. While I think you really have to try hard to get your phone to permanently stop working, I have never heard of anyone successfully wiping the stock system with another working rom. It didn't work for me on stock ics, and I most def wouldn't recommend trying it over JB. Right now I am on the JB stock, with a bunch of apps frozen. Everything works, except for a glitch with the shift key. Give it sometime, things will start streamlining here pretty quick.