Take a closer look
If you have two parties playing the campaign, one aiming for high (good) reputation, one aiming for low (evil)....is it possible that one of these parties will become locked out of the campaign missions in some way?
Some scenarios do change the state of the game world in a major way. So, yes, you will definitely close of some scenarios if your parties play in the same campaign.
If you dislike your parties interfering with each others, you will have to keep separate campaign states (documents for which you can find in the Files)