You have to realize that Ducky has probably been in worse situations than that. For example, in the very first movie, she is chased by Sharptooth to the point where she is riding on his nose. Also, in LBT IV, towards the end she is pulled from both ends by Icky (pardon the spelling) and Petrie, but then dropped into a river, flung into the air by Dil, and then lands on a small tree branch which bounces multiple times. If that doesn't make her throw up, then I'm not sure being in a tree as it falls off a cliff will really cause nausea. Now maybe if the tree were spinning then that might cause nausea from being extremely dizzy.
But to be plainly honest, I really don't find making characters so loved by little kids put in extenuating pain like that very appealing. I mean that's what the purpose of a fanfic is, to make your own idea on an existing franchise, but does a character really need to be blinded by some sort of poison or throwing up after a near death experience? I'm probably contradicting myself because in Revenge I there is a near death experience, but the characters come out fine in the end, just extremely tired and worn out.
I realize this is your idea so don't let my opinion keep you from making this fanfic

. You can do whatever you want with it, as long as it's logical. I'm just throwing in my two cents on the matter thats all.