I'm currently playing Alpha Sapphire and I fainted Kyogre before the Elite Four. So after I defeated the Elite Four I encountered it again and I fainted it 'again'. So after I defeat the Elite Four a 2nd time, will I be able to have a rematch?
I'm now really scared if I can't get a Kyogre and will have to redo the game.
Of course. You can do this as many times as necessary to find Kyogre. You just have to keep beating the Elite Four if you do happen to defeat it.
Please remember to save before fighting Kyogre next time.