covering up the hole initially, so that you cant fall through it, doesnt feel logical to me, since Gus fell through it as well. (or to make this work within the game-logic, the whole cloud/hole-Design would have to be changed somewhat). Thats why i would prefer that you can fall, but not hit him - his branch swinging to the side from his impact/weight seems reasonable to me.
I didnt have that Problem but sure would have hated to solve the Puzzle accidentally. I also think it would be best, to add an additional step to the Puzzle so it isnt possible to free Gus before meeting him. How about the Branch/Root he hangs from got bent (by his impact) and is now stuck a bit to the side of the Falling path. To hit him, we would have to get his branch free again, so it swings back to its original position under the hole. This might be done by simply clicking on some other obstructing branch, or Even involve a Tool we need to get first. If we fall through the hole before readjusting the branch Gus might say something like "that was close!".