"To separate" in time context

Solution 1:

If the item that separates is being emphasized, it can be used in this way. For example, I could say, "my home in the Midwest US is separated from Europe by the Atlantic Ocean." In fact, there's a lot of land between us too, and some mountains as well, but I'm pointing out the fact that the ocean is the biggest obstacle between us.

Perhaps your colleagues are referring to Wednesday fancifully as though it were an obstacle or wall between two locations, making it impossible to get to Friday without going through the boredom of Wednesday. Office small talk often consists of different metaphors for the weekdays, since it's something everyone has in common.