I’d use Dynamics. Go to Project Settings (Ctrl(Cmd)+D) > Dynamics > General tab and reduce Gravity to 0 cm, then add a Rigid Body tag to your Cloner and under Collision tab, set Inherit tag to “Apply Tag to All Children” and Individual Elements to “All”, Shape to “Moving Mesh”, then under Force tab, change Follow Position to “5” and Follow Rotation to “5”. You will need to experiment with these numbers to get the visual look you desire.
The clones will then bump into each without intersecting.
To stop them moving in a certain position for the piece, Bake the Cache for the Cloner (Rigid Body tag > Cache tab), move to that position and right-click the Cloner and choose Current State to Object.
A simpler alternative, depending on your coffee bean geometry, would be to use the Push Apart Effector, but you may not get the result required.