I know you love Rhaegar and his intention may have been good but he screwed up things royally. Being married, took another because he was obsessed with prophecy. Knock her up, start rebellion and basically lead with Aerys who did worse things but still Rhaegar contributed to fall of his House. Their love as Rhaegar and Lyanna cost thousand of people their lives and it was immature from them. Especially from someone clever, responsible like him. He should've known better.
I think in some point everything was meant to be. If rhaegar and lyanna wouldn’t have run away, then jon wouldn’t exist (the prince that was promised/azor ahai). The stark kids wouldn’t exist (the three-eyed raven), the dragons wouldn’t exist (daenerys wouldn’t get the dragon’s eggs, and she wouldn’t give them life), so the apocalypsis would come and everyone would be so screwed. Yes, a lot of people died, including him, but thanks to that, a lot of people may live as well, and the living have more chance to win that war.