I find this a very interesting question.
Apart from the fact that the above sentence sounds strange, as Alex explained, when one reflects on the two sentences, the differences in the meaning and emphasis are quite interesting.
It's more or less similar to the difference between 'the text is unclear' and 'the text is not clear', for example, or between 'you are a woman' and 'you are not a man'!
I feel that 'you are without us' is somewhat passive and doesn't 'lay the blame' on the person being addressed as much as the original sentence 'you are not with us' does.
I can imagine the context that generates each sentence to be vastly different.