The souls were no threat to Castiel – the Leviathans, however, were. That's why he blacked out in the campaign office and killed everyone present. He just couldn't control them, so they hijacked his vessel. And by the time Cas got rid of the souls again, he was already so weakened that the Leviathans had no problem overpowering him for good.
The Leviathans were too strong for God (the first, original God) to control: that's why he locked them in Purgatory to begin with. They aren't just your average, everyday, human soul. They're much, much stronger than that. I would find it hardly believable if Cas (who'd only been God for a short while) would be able to instantly control them -- especially while controlling all the millions of other souls he had inside him.
