I absolutely don't think that she wanted the twins back with their father. That would be a happy ending for them and there is nothing she hates more than a happy ending for anyone but herself.

I'm sure she thought that they would be killed or injured and that she could pin the blame on Emma. At the very least Emma would lose her position as sheriff, and, if Regina was lucky, Emma would be killed or injured herself. (And she would definitely have no trouble harming children considering she sent several of them to their deaths in FTL.)