My advice on Little Snitch is not to be discouraged by the constant warnings. After a few days marking certain things as "always allow" or "always deny", it will not be a major nuisance.
True, you cannot make it 100% secure, since it's always possible to exploit one of the programs that you must allow access, like mDNSResponder.
There's only so much you can do with software. Do you have a good hardware firewall?
As for editing files, you can do it with command-line tools like vi or nano (using sudo when necessary to edit root-owned files). Personally, I like to use
TextWrangler, which is a nice friendly GUI app that lets you open invisible files and also save files that require root privileges (prompting you for a password, of course). If you need to make your own .bashrc file, make sure to set the line break style in TextWrangler to "Unix (LF)" (there's a menu at the bottom of the window, next to the scroll bar).
At this point I wonder if I should go back on my previous recommendation of keeping the BSD subsystem. I'm honestly not sure what all would break if you removed it. It's worth looking into, though.