"Protocol" is simply the official description of the rules for VAR.
I agree that it was an easy decision yesterday, but the problem is where do you draw the line? You don't want the VAR to be arguing about 50/50 or 60/40 challenges for a simple foul, or even a yellow card - they may have importance, but they're much more common and much less important events than a red card or goal. So, would you say, only when it's really obvious...or maybe "clear and obvious"?
And that's the problem - how many discussions are there about what a "clear and obvious" error is, and how many times does "clear and obvious" seem to depend on the team people support? Yesterday was an unusually poor decision, but it's an outlier - I doubt we'll see another decision like it all next season, but if we change the rules we might see a lot more marginal decisions argued over endlessly.
All that might not make sense to you, but the thing to remember is that VAR isn't there to fix all decisions - it's been decided all over the world that it will only look at the major ones, and we leave the others to the ref's on field decision, even though we know they'll make mistakes. Introducing a rule that only applies to the really obvious ones, isn't possible, and given how much controversy VAR generates, they'd be mad to try and introduce a rule which only affects some yellow card offences, but not others.
On your other point, the ref would have to stick to his original decision. As soon as it went to review yesterday, he must have been told/realised that he'd make a mistake, so seeing it doesn't change the rules he has to follow.