My cat has 5 week old kittens and "disciplines" them quite harshly...?

She may be having a rougher time with this litter based on where the genes of the father of this one came from. If it was a more ferral cat than the first father, then these kittens may be presenting more of a problem to her than she is used to. Cat personalities can also be similar to a human in the amount of attention that must be given, and she may just be fed up with the antics or she may have a cat version of "post partum" if this litter came too near the occurence of the first and she feels a type of depression over it.