2 solutions i can think of off the top of my head without digging into your file.
1. Assign the low walls onto a different layer (for example in our office - A-WALL-INT vs. A-WALL-INT-LOW). This allows you to assign a different layer "group intersection number" to that layer, therefore they will not clean up. Don't forget to lock the number into your corresponding layer combinations.
2. Manipulate the building material priorities in such a way that your tall walls are stronger than the materials in the low walls.
Both probably take some trial and error, and might force you to create a new layer or building materials. No big deal, you just have to determine what makes the most sense for your project.
-mb