I think stability as a discrete thing can work if there's feedback between it and bad events. If low stability causes bad events (or at least, makes them more likely), and bad events lower stability, then stability does in fact function as an overall indicator of the state of your nation, avoiding the incongruity you're describing.
I know what you are saying but I still don't really agree. I think that it all stems from different perspective and mixing up cause and effects. Let me try explaining.
The events that you described are already what means that the country's stability is low. If there's a revolt, then that's an intrinsic change from positive to negative in country's stability. On the contrary, if- for example- estate's loyalty/happiness changes from negative to positive, then it's an intrinsic increase in country's stability. Changing some stability value on top of that, even if as the result of some event, is nothing more but an arbitrary penalty (or bonus) applied to the country, on top of bad (or good) things that are already happening. Hence, stability should be perceived as a current representation of past and ongoing events, and nothing more. If the events on their own are not enough, and an additional modifier in the form of stability mechanic is
seemingly needed, then "seemingly" is the key here. That stability mechanic is not needed, if anything, events' effects (both positive and negative) should be magnified.
Another example would be inflation figure in real world (which EU4 also gets wrong). People often have wrong perspective, and see inflation figure as the cause, rather than effect. Inflation is a figure (an index of sorts) representing
past changes to prices, not the current or future changes. In other words, prices don't change because of inflation, inflation changes because of prices. (Note that here I'm focusing on the figure representation inflation, e.g. 5%, not the inflation phenomenon itself which is an increase in prices over time, just like stability is a result of changing situation in the country over time).
I see inflation and stability in the same category really. So if "stability" exists in the game in any explicit form, then the best place for it would be the ledger IMO. The game could calculate the stability index for each country based on may factors such as devastation, internal turmoil, ongoing wars or lack thereof, etc. But stability figure would remain just that- a figure representing the internal stability of the country, and not an arbitrary scale for positive and negative modifiers.
EDIT: Added some clarity about the inflation to avoid confusion between the inflation figure and the inflation phenomenon.