If a unit is already in rout, from earlier activation, and manages to make it through to another activation, can a character then join the unit to make a valient unit again?

It depends, some units cannot work with some leaders. Of course they would have to rally before anyone could join them at all.
Some examples are the Brets have a virtue that doesn't allow the character to join any unit, the Wood Elves have a kindred that does the same. I am not aware of any flying units that can be joined by characters, etc. Check your codex for details on your army.