The same reasons most youtubers stop playing the game:
1. As the Grumps were so careful to note on their Steam Train playthrough, when they asked for permission, they learned that the creator is generally okay with Let's Plays, but he wants people to experience it for themselves. If you watched your favorite youtube personalities play it from beginning to end, what would be the point in playing the game and learning how it ends yourself? I mean, it's not like it really offers much in the way of gameplay. Story is the biggest thing Undertale really has going for it, so if Markiplier finished the game, that would take the experience away from thousands of people.
2. It's really fucking hard. The hardcore "Practice 60 times before filming"-level walkthrough guys die nearly five times a video on the final boss(es). Have you ever tried playing a high-level bullet hell game while doing voices and hamming it up in front of a camera? If Markiplier did 3 endgame videos of Undertale, unless he was awkwardly silent and focused the whole time, I doubt he'd have the time to make any other videos. It would be that sewer game that nearly drove him insane all over again.