For those on emulator I found a way to at least not get it to crash when hitting the water and getting your item:
Backup and change links instance + 0x134 u32 ActorMain to 0, pick up item and change it back to original value.
Less complicated (if your purpose is simply to play around with GIM and test stuff), go get the Slingshot and you can perform GIM with Deku Seeds (doesn't crash).