You mentioned in the beginning that there will also be mission disks for SQ42 (at least one).Will a character be able to go "back" to do these mission disks of SQ42 after finishing the "original" campaign and moving on to the PU?asked by Gebu

Yes, absolutely.In fact, the additional Squadron 42 story packs or whatever will be written and designed to be such that they're expected to be after you've finished Squadron 42 and you've mustered out into the great galaxy as a whole.So you definitely will be able to go back to them after finishing the original campaign and beginning the Persistent Universe.