Well, I waited until November, and journeyed to the Fruit Tree Exclusion Zone. As I'd hoped, the game didn't crash this time. After a bit of searching, I found this spot. There's a mature pink apple and a young pink apple growing very close to each other, flanked by a maple and an oak. They still had some leaves on, but whatever was causing the problem wasn't there.
I chopped down both the apple trees. Of course, I won't know if that fixed the issue until next summer, but I have a good feeling about this.