You added it to your PATH and didn't get any results? Windows only looks in directories specified in PATH.
Having to switch drives shouldn't be an issue. I run Cygwin, Python, and Ruby form a data drive, but have my profile on the system drive.
You could write a batch/python/ruby/perl/cygwin-bash/whatever script like AutoBot is suggesting that takes 'Game1 resourceconfig.xml resources.swf' as arguments, and knows to look for a directory named src in D:\Program Files\dev\Game1 and run samHaxe on the files there.
Another option would be to just start a cmd (or bash

) shell and set your samHaxe path equal to an environment variable named something simple like %SH%. Then you just have to type "%SH%\samHaxe" resourceconfig.xml resources.swf.
I'd personally recommend Python or Ruby first, and bash/cygwin second, but only because batch scripts look ugly as sin to me.