Wu trained Morro at the same time that Garmadon was training with Chen which MEANS that Misako was around to see what the pressure of wanting and training to be the Green Ninja could lead to.
So later when she had Lloyd and KNEW that he would be the legendary Green Ninja, do you think she thought of the child Wu had once trained? The kid who became so obsessed with proving himself that he put himself in danger time and time again? The little boy who ran off into the night and never came back?
After seeing that, is it any wonder why she didn't want to leave her son-- the actual Green Ninja-- to be trained by Wu at such a young age?
Maybe a boarding school for bad boys would never make him want to be a hero. Maybe it would keep him safe from the destructive power of destiny. Maybe Darkley's was the only way to save her beloved son, Lloyd Garmadon, from himself.
Maybe Misako remembered Morro. And maybe, just maybe, she knew it would be best if her son never turned into someone like that.