They aren't penalizing you without good reason. Comets are an abstract stand in for the various events and actions in a nation that a ruler has no control over, and decrease the stability of the state, weather that be idiotic politicians/nobles who scheme for their own advancement or a devastating hail storm that ruins the crops. It's just that, instead of making a myriad events to represent each one of these individually, they get lumped together under comets. 0 Stab is what you should be at most of the time. Going above or below that is the exception. Furthermore, it is harder to gain or maintain order than it is to lose order, that's the nature of entropy, and why you are more likely to receive events that lower stability than raise it, especially at high levels of stability. Making this non random allows the player, who is much better than the AI at abstract thinking, to game the system and have perpetual stability, unlike any nation in history. And make no mistake, this game is in part a history simulator, not a "I overpower all of my foes and never lose or have bad things happen to me" game.
I'm sure that was their thinking "it would make the game too easy" but it's nonsense!
Look, it's simple: condition -stab events to things you might want to do (royal marriage for instance). There are already lots of such events (your nobles get pissed off by your modernization program, traditionalists are offended by your modern military tactics, etc.).
Just link these events to player decisions. What are you going to do?
Not modernize because traditionalists won't like it and that causes unrest?
You want to improve your trade power, so you invest in diplotech, but this increase in the power of the merchant class brings them into conflict with the traditional nobles.
Also, modernizing the military means relying upon mercenaries and standing armies instead of feudal levies, which means that nobles have their military obligation converted into a tax owed to the king. That plus centralization brings the new nobility who may have obtained their patents of nobility from royal service to the crown, into conflict with the older traditional noble families.
Virtually everything you might want to do is going to cause conflicts with somebody, because what the game is modelling is
change and modernization. Well, those who are already at the top don't like any changes, especially when it means they are going to lose out!
So, virtually everything you would want to do to increase the power of your state and expand the size of your country is going to cause a stability hit in real life.
This could easily be modeled in the game. Instead Paradox took the lazy way of random events.
Yes, it models some of this, but what is objectionable is that it's not tied in any way to player decisions.
Your point that it would make it too easy for the player to avoid is nonsense because the decisions that would cause stability hits are exactly those which any enlightened monarch
would want/need to take and which cannot be avoided unless you are going to stagnate and become a victim of more forward thinking and aggressive neighbors.