Without knowing how the frowny face is explained to the children, and how they feel about it, and how the teacher interacts with them in general, it is impossible really to comment.
It may be a really negative thing for children to experience, but on the other hand, if the relationship is right with the teacher, it may just simply be a system of communicating an 'oops what happened' comment without writing a note. I would look at the whole picture, not this tiny aspect of the teachers classroom management! If it is part of a policy of humiliation fo children, then it is terrible. If it is simply a way of communicating a simple point - your homework is late - I dont see that as being damaging to a third grader.
The issue of homework itslef is a separate issue that parents need to talk to the teacher about. I am supportive of homework if it is meaningful and useful. Not if it is simply a time filler. That is where my focus would be. If the homework is reasonable, and if you have communicated with the teacher that you support her in getting your child to do it, then if your child gets a grumpy face on her work, then let it be a lesson to her that she should have been more organised and done it. I dont' see the big deal, personally.
If the child hasnt done the work because of a good reason, then I think it is the parent's responsibility to communicate that to the teacher, by note, email, call etc. Again, that is a separate issue.
I'm sure there are some fabulous, motivating teachers who would put a grumpy face on a piece of missed work. And some terrible teachers who would never do such a thing. The quality of the teaching and relationships should be the issue, not a system of communication that may well not upset the chidlren, only the occasional parent. Sometimes children are much more open to such simple systems than we as parents would think.
I'd go in, get the background, and iron out your differences about the homework before making a judgement about the spirit in which a grumpy face should be taken.