Hmm, if you setup your account properly, then go into your account in K-9 so you see all your emails. Then hit the menu button -> folder list. Then in that screen you can hit menu -> create new folder and such. Then if you go back to your inbox, and you long press on an email, you have the option to archive, delete, move, send, forward, etc. So then you just click move, and it'll let you move the emails.
Edit:: I just reread your post. I don't think it allows for automatic sorting. Technically if you set up automatic sorting on your hotmail account online, it'll sync to that folder in K-9. So for instance, if you get a mail on your hotmail account and it goes to your inbox, k-9 will show it in the inbox, but if you set up a rule to automatically move this mail to your "other" folder on your hotmail account, then in k-9 it should show up in that folder and not the inbox.
I think, haven't tested, but makes sense to me.