I've did this mod to my cradle a long time ago, with no problems since, but you're right, Mocha won't work then.
I've got a serial>Palm lead that I haven't modified that I use with VNC and in the car. The cradle wasn't practical to use in the car, anyway.
It's amazing the difference it can make to the battery like. Make sure you've got 'beam recieve' switched off as well (unless you need it), and the batteries should last a long time.