To my knowledge:
Military losses do not affect moral. You can, of course, roleplay some moral effect (SM Mode, F2 screen, SM Mode button, Unrest Points)
Moral is negative affected
-If there is not enough Infrastructure for the populations, so people are dying in the streets
-If People feel not enough protected (warships/PDCs) from creepy aliens
Moral affects productivity. I belive there is a direct relationship, i.e. Moral 90% --> Productivity 90% but I am not sure about this.
I don´t think rebellion is in as of yet.
Typing this answer made me realize, I don´t realy know a lot about moral and its effects