I did this same thing, but instead of using the power line, I just put the switch on DS0.
Both the drive and the Gotek were always powered on, but the switch controlled which one was the active drive.
Worked great, but my cable w/ the switch was UGLY.
I've been meaning to do that again possibly, but I have to figure out where I would put my Gotek. (In my A1000)
Although my Amiga 1000 internal floppy is really unhappy. So I'll also need to sort that.
http://eab.abime.net/showthread.php?p=946881&highlight=switch#post946881(Note: ignore my comment in that post about the Gotek supporting a Kickstart, as it does that fine. I had a bad image/transfer at the time.)