Can a jailbroken iPhone and a non-jailbroken iPod Touch operate on the same machine/itunes
Sure, it'll be fine.  I did that for a while after I got my iPad and still had my jailbroken iPhone 3G.

Jailbreaking, at least at its basic level, doesn't mess with most of the basic functions of the device such as syncing.  All bets are off if you install some JB app that is specifically meant to alter some part of the sync process, but even then it's very unlikely it will cause trouble of the iPod.