I think it's a kind of claim, I think John tried to say "Hey, please stop fighting, stop this storm"
I'm not American so I don't know many thing about American history, but we all know the Vietnam War, the New Deal,etc.
I think it was dedicated to those people in the Vietnam War, but for me it could be also for all the Wars around the World.
What kind of song would John write for our actual world? Who'll stop the rain is almost a hymn.

Still the rain keep pourin', And we all still wonder Who'll stop the rain?