What a lot of people tend to forget is how far ahead of its time that Miami passing game was.
Chicago's great defense was designed to stop the run first, force teams to pass, and then send everyone. Marino's quick decisions and release were too much for the Bears. Nat Moore, in particular, was open virtually every play. How would Chicago have adjusted? Like you noted, by trying to pound the rock with Payton and limit the Dolphins offensive plays. Would have loved to have seen a rematch in the super bowl.
Even the great Bill Walsh figured out that you couldn't beat Marino and the Dolphins with a conventional approach, bringing in as many as seven defensive backs in the super bowl. I believe he did that in the second quarter when Miami was up 10-7 and Marino was absolutely destroying the 49ers. That SF team was loaded with all-pros on that D, but had to go in a completely different direction to slow the Dolphins down and, ultimately turn the game in their favor.