You are right that 11 games isn't enough time for Assad to greatly accumulate a meaningful amount of additional WAR than another pitcher. Though I would say that by being a metrics beater, ZIPS is naturally going to undersell Assad (though initial point remains). Also when we are talking such a small sample, one mistake, one bad inning, etc is going to have an oversized impact that you can't really account for with WAR. Sure that also means Assad can throw a bad pitch with the bases loaded and give up a grand slam where Rea might have induced a ground out. But in general, I'd trust the pitcher who has performed better to be less likely to make that mistake.
Bottom line for me is that the depth doesn't really matter. Given who is coming back, it would take a significant number of setbacks for the loss of Civale or Rea to make a difference in the Cubs season. I'd prefer to maximize the chances of winning the division by remaining incrementally better, not sending down Assad to protect a player who is probably going to be DFA'd in a couple weeks anyways. Will it make a huge difference? Probably not, but the downside is minimal IMO.
But agree to disagree, I understand your points and they make sense logically, I just don't think we need to protect a pitcher who is likely not long for this team anyways at the expense of continually sending Assad down and then back up again when he has performed in every season as a big league pitcher.