If all civilians are killed or if all tech is destroyed, that would be a loss to Phoenix Point and no experience points or reward should be earned. The only reward if killing all attackers after it should be the non-destruction of that Haven.
If objectives fail - Lose Havens rescue and destruction mission | Voters | Phoenix Point
The main objective is to defend the attacked facility. The haven is more than the tactical map, you are fighting at. So if pandas attack the energy facility, you defend the energy facility. Other facilities are not target of the attack and won’t get damaged.
You already don’t get XP for the objective, if you lose this objective. Since you defend the haven, even if damaged, a reward is fine.
Some facilities, like the anu energy facility, have very few objectives close by, that can be destroyed by pandas in 1 round.
If you change the mission reward as you have stated, it will encourage players to maximum abuse the classes for maximum profit and will harm build diversity.