The magnet only exists to attach the antenna to metal surfaces, so theoretically you should be able to use it without the magnet. I've never tried to take one apart, so I don't know how difficult it would be to remove without damaging the antenna.
The PhidgetGPS should work with any GPS antenna with a SMA connector on the end, so you may be able to find an antenna from another website that doesn't have a magnet inside it.