There may be methods that doesn't require aniamtion nodes, I will test that later. but here is what I thought at the most beginning and has been proven to be working:
Theory: using locations of particles as a guide for rigid body objects to set in their places. The intersection will be prevented by rigid body dynamics.
Add a particle system to a mesh. (...
I just tried something similar and it worked OK, I'm guessing your spheres are too close / touching on the initial frame. This will upset things.
Here's my result-
And here's the scene-
If you move my spheres so they're touching/...
I red the question, but since it's a bit confusing for me (so many steps) I sticked with title - to solve passing objects, with a file you provided.
Start position of leaves comes from particles behaviour (they collides only in circular shape. Enabling Rigid Body to these leaves results in move ("explodes)" them down. In a Rigid Body World, there is ...