I don't think that on previous alphas jumping and running affected the timer, or did it? Could be wrong.
This is a bigger problem in the early game if you don't have a vehicle and need to move by foot.
Most POIs require jumping to get around.
From a survival game "on paper" standpoint this is fine, you made a mistake and you suffer the consequences.
From a gameplay / enjoyment standpoint I find it hard to argue against that it is pretty ridiculous. 40+ minutes in real time is harsh. I dunno, maybe not a problem for the hc gamers who play multiple hours a day. I don't see it as a challenge. If you're semi-forced to mine or spend time crafting or upgrading the base / do whatever you can without moving much, I find that it's just a change of schedule - you probably would have done that anyway but at a different time.
If I was to change it in any way, just cap the player speed to a slightly lower value instead of adding to the timer. Add a pain sound if you were to keep the health penalty when you jump to have some indication that you are actually losing health. Or have some sort of threshold that you could run for a bit and jump a couple of times before it starts to hurt or affect the timer. Right now the debuff is very... crippling
TL;DR
I'm ok if it stays as it is but there is room for improvement to make the leg debuffs less anti-gameplay.