Thanks for the reference! I found a writeup on it at
www.constitution.org.
Although I need to read and digest it fully before rendering my final opinion on it, my initial impression is that it was a bad decision.
The Commentary by Jon Roland which accompanies the decision, and appears both well-informed and well-considered, agrees with my impression.
Just because the Supreme Court has decided something does not mean it's right or constitutionally correct, nor that it can't be addressed by Congress, the states or the people in the future. It is binding until overturned, but it can be overturned.
History is rich with examples, both current and ancient, and this seems to be one of them.
Roland's commentary is not persuasive and, in fact, adds evidence that Marshall's ruling was consistent with the intentions of the Founders. Madison's attempt to have the BoR extend to the states was explicitly rejected. And there is no doubt that many during that era were not inclined to give the federal government extensive powers over the states which extension of the reach of the BoR would have clearly down.
Marshall's noting that when the Constitution meant to indicate restrictions upon the States it made that clear is consistent with my understanding the language of the 1st notwithstanding.
As far as the "selective application" argument goes there is nothing within it which means that the areas where such application is in effect are wrong. It may be concluded that those areas should be widened which is not likely the desire of the author (or you.)
Since the BoR has now been extended to cover the states it appears the point is moot.