get the excluder off at least until the bees are working the boxes.
even if the queen were to lay there, so what? unless you are doing cut comb, it makes no difference. most of the time, she doesn't go up there because there is already honey over the brood nest and most queens don't go over it. if she does, and you want the brood out before you take honey....which you probably shouldn't be doing the first year....you can run her down, put the excluder on, wait for the brood to hatch and take the super.