If only Milk-sensei would dress up in a maid outfit too...
This was Weiss's mistake, basically. He should have planned this from the beginning, first the girls in maid uniforms, then the boys. For the girls' half, he should have prepared a maid uniform for Milk as if it was the most obvious thing in the world, giving her the uniform with perfect coolness, not asking any questions, just telling her that she will be the head maid among the girls.
Besides, it had to be divided like this anyway since the intended clientele would be two very different groups, so not having both girls and boys in the maid uniforms at the same time would have been easy to explain to even someone like Milk.