It's not so weird.
In the ACA case, the court simply used a test that applied logic to the whole of the law, instead of a single sentence. This is not unusual. It's not that words lack meaning, it's that few legal codes are perfect and it's a judge's job to figure them out. SCOTUS did that, in line with the role set out for the court in the Constitution.
With regards to the Rebel flag, it's more accurately called the Battle Flag of the Army of Northern Virginia. It was never adopted by the Confederacy or any Confederate member state as an official symbol.
The fact a bunch of people want to treat it as a cultural symbol has always come with the understanding that it's also been understood as a symbol of oppression by many, many others.
It's ironic to hear judicial literalists claim an ambiguous sentence should be used to strike down a major piece of legislation, then turn around to defend the "Rebel Flag" as something worthy of cultural status. It never was a cultural symbol, it was the standard of an army that has little relevance to any actual antiquarian interested in the identity of southern states.
As far as changing the name of a park goes, monuments are retired all the time. Consider the case of Fort Haggerty:
The history described there is actually inaccurate, the fort was actively used through WWI for ammunition storage. But regardless - it was named after a predecessor of mine for his gallantry in battle against that same Army of Northern Virginia. I am not sure how fair it would be for people in Virginia to have to live with that Fort there today, considering what happened during the madness of war.
The point here is that there's often a difference between the literal truth of a matter and way it is interpreted by the many. It's useful to consider other points of view before declaring the world's gone mad.