Well, most of the time, they do act like the traditional Macguffin; until we go into their back story, all we really need to know is that Xykon wants them, and it's bad news if he gets them, but it's kind of a shame to just destroy them outright. Otherwise, the Order could have been guarding books or rings or jars and the only other requirement would be that they couldn't move them without risking the cookies going stale or something.

However, the gates' back story is also called upon for foreshadowing and world-building purposes, so they're not JUST macguffins, which is nice. I guess it kind of depends on your definition of, "interchangeable," as to whether they count at all.