May which ever squad created the alliance automatically gets their hours added. But squads that joined can't add their initial hours when joining the squad, only the hours they gain while in the squad count. I think this would even it out.
Squad A has 250 hours and makes an alliance. So 250 hours go to the alliance. squad B joins with 100 hrs. The alliance still has 250 hrs, but squad B bases after they join and get 10 hrs that day. The alliance now has 260 hrs.
I realize a lot of you will dislike this but it seems fair in my eyes.