I’m pretty sure he wasn’t expressing support for atomic power. And the song isn’t simply about slavery, but more about Rastafarian beliefs in general, which include many Afrocentric and Pan-African elements.
As for the meaning of the atomic energy line, my take is that it reflects confidence that Rastafarian prophesies will come to pass and that no amount of atomic bombs will change that. The lines that immediately follow are:
“How long shall they kill our prophets,
While we stand aside and look?
Yes, some say it’s just a part of it:
We’ve got to fulfill the book.”
Brushing away fears of the “atomic energy” bogeyman just reflected his strong belief that “the book” would be fulfilled and God’s chosen ones would live forever after. In that context, why worry about some piddling nukes?