There's a commuter specific forum (
http://www.bikeforums.net/forumdisplay.php?f=20) that would probably be more helpful. But a few tips.
It's going to be up to you to decide wether or not the route is too dangerous for a commute. My mentality is that if there's an alternate way, even if it adds some miles, use it. There is going to be a line where the additional miles becomes too problematic compared to the additional safety you aquire, so it may take some time to find the perfect route. As far as bike safety is concerned, you can never fully protect your bike so commute with a bike that you can stand (or afford) to lose. There was a thread about this guy that had is bike stolen in the commuters forum that I found interesting:
http://www.bikeforums.net/showthread.php?t=129632. Good luck, and I hope it works out for you.