You need to specify what you wanted synced to each computer, with no "overlap."
In iTunes on both the mini and MB, uncheck "Automatically sync when this iPhone is connected" and check "Sync only checked songs and videos." In iTunes on the mini, go to the Music tab and select "Sync Music." Select whatever else you want to sync from the mini. In iTunes on the MB, don't sync music or anything else that's being synced from the mini.
I did something like this for quite awhile before Exchange support came in with v2.0 of the iPhone software. I used to sync Calendars/Contacts from my work PC and music and other media from my old iMac G4 at home. It worked fine as long as there was no overlap in the sources for each type of info that went on the iPhone.