I think that it couldn't have continued, not with M&S anyway. Too much had happened for them to just go back to doing regular cases.
Unless it was then on the run, what happened to them in the weeks and months following Mulders jail break, how they got their lives back (well, Sullys) and the effect it would have on their relationship. With that it's quite restricted to what you can do. So I think they were right to end it where they did, and let M&S run off into the sunset and let us wonder what happened to them and if they stayed together or not.
If they were to continue with D&R they could pretty much just do MOTW and build a new mythology and appeal to a whole new fan base. But with TV even more cut throat these days than it was back then it would have to be pretty damn good.