As outlined in a comment above, I'm inclined to agree with DavidT that trying to use one root balancing value across a diverse range of games is unlikely to be practical. Even when you allow for each game to adjust those values on import, the amount of one-off adjustment that would need to be made to fit well with the experience of each game is likely to outweigh the benefit of having a standardized input scale in the first place.
That said, if we had to pick some at least plausibly-principled basis for such an input scale, what's the best we could do?
I posed this question to a colleague who used to work in modelling and analyzing the impacts of weapons, explosives, crashes, etc. for the UK Ministry of Defence. They pointed me to Criteria for Incapacitating Soldiers with Fragments and Flechettes, a now-unclassified 1965 report by William Kokinakis and Joseph Sperrazza for the US military. My colleague described this as "the backbone of all military survivability/lethality analysis."
The full report is around 90 pages and too much to summarize well here. Its main approach to quantifying injury is to estimate a probability that a particular hit/wound will incapacitate a soldier, keeping them from performing some tactical role.
It includes formulae and parameter values to compute these probabilities from the projectile's mass and velocity, similar to the kinetic energy formula you gave, with varying degrees of complication depending on the scenario, part of body hit, clothing/armour worn, etc.
You may be able to use this probability as your standard measure of damage. When you need to compute a probability for a scenario not covered in this report, you can search for reports citing it that cover the scenario of interest to you: they should have what you need to convert answer into the same probability terms.
Exactly which number you use will involve some arbitrary choices (e.g. do you assume limb, body, or head shots, or some particular ratio of each? Do you assume a target who's nude, or armoured? At what range? Are they in an assault or defence role? etc...) so unfortunately you'll still have to put your thumb on the scale somewhere when boiling down something as complex as physics tearing through biology into a single number.
Since we ultimately need to make some arbitrary choices anyway, I'd argue in favour of making your arbitrary system as simple as possible. If you can pick a number for a weapon in a couple minutes instead of hours of research, and if a game developer importing your weapon can do so without having to read and understand a 90-page military statistics report, then your proposed system has a better chance of getting wider support. The more technical you make it, the harder it is to create content for or implement into a game. So the arbitrary-unit 0-100 scale has a certain appeal there.