I think the whole "you have such a pretty face" thing is just so rude. They might as well finish the sentence -- "you have such a pretty face but your body sure is ugly". Well, er, thanks for the compliment!
If my boss said that to me, especially in front of coworkers, I would really want to say, why the heck to you care if my face is pretty, or puffy, or just plain ugly? What's it to ya?
I'm sure she meant it to be nice, but that would irk me. It's so demeaning! Why not just say, wow, you're looking really great, congratulations on the weight loss!