I've deployed over a network and didn't have the problem with switching disks.

IIRC, there are some options available on the setup command line.

Deploy MapPoint over a network or

KBAlertz.com: MapPoint: How to use Administrative Setup to install MapPoint 2006

Gives some hints. I haven't had to do this for quite a while. I remember having to do it because the machines didn't have CD drives (security reasons).

The trick to doing the install from a flash might be to copy the files to the flash (as you would to the network), then use the admin install options.