Throwing daggers instead of rocks at the rock pile by the bansai tree prevented the animation glitch/crash for me. As a thief I read online about an alternate solution of using your grapnel hook to climb to a ledge above the bansai tree then use the hook to fish the tree up but the game kept saying I'd destroy the tree in the process. Knocking the rock pile down ends up washing the bansai tree down where you can simply pick it up so I have no idea how climbing above the tree helps.

Either way throwing daggers solved it for me.

EDIT: Sweet, I figured out how to use the alternate grapnel hook thief method. While on the lower section use your grapnel on the rock pile as if you were using daggers or rocks. This will dislodge the rock pile but the bansai tree will NOT wash down like the other methods. You must now use the hook to climb up the ledge and then use the hook again to 'fish' the tree up. "You've caught a big one!" =-)

I don't know about how to solve this puzzle with other classes but besides the bugged rock throwing method daggers or the above described grapnel method both worked for me as a thief.