In my opinion (formed after re-reads, research, and even asking around)- the original negative r-project.org article is wrong on some of its key technical points (for example: there is no C++ interface to R, article fails to emphasize Rcpp properly uses the C interface, article doesn't mention important history of .C versus .Call, and so on) and does not support a clear conclusion (let alone a conclusion of "don’t use C++ to interface with R"). I respect that the article is coming from a knowledgeable R authority, but feel the article has not been a good thing for the R community.
If the article had been carefully labeled as being only about "writing C++ programs that make calls to R" that would have helped. But it is hard to support that position as the original article starts with "About 20% packages from CRAN and BIOC repositories include some native code and more than a half of those include some code in C++". That commonly means R using C++ for extensions.
Perhaps the article should have been on a personal blog, or r-project.org should become a formally refereed source (if one is going to treat it as authoritative).