If It is a limited amount of work you have in mind, pull the subfolders out of the folder and onto the bookmark bar until the folder is empty, and then put them back in, in the order you want.
For big folders, this is a nuisance, but for small cleanup work, it's an idea.
In TIdy Bookmarks for Chrome, the folders can come out alphabetically on the personal bookmarks bar, and items within the folder do also, but not subfolders. Those, one would have to play with if it's important -- along the lines of what I suggest.