Your analysis of that article does seem a little skewed in my opinion. From your link, emphasis mine:
"In a 2008 article in Science called "Reassessing HIV Prevention" 10 AIDS experts concluded that "consistent condom use has not reached a sufficiently high level, even after many years of widespread and often aggressive promotion, to produce a measurable slowing of new infections in the generalized epidemics of Sub-Saharan Africa."
Thus it does not seem to be accurate to say "condom use has not found to been to be effective protection against HIV/AIDS" since part of the issue seems to be that not enough people in Africa are using condoms. It's like saying 'antibiotics have not been found to be effective against infections' in a situation where few people are actually being given antibiotics.
The article does support a two-pronged approach: promote the use of condoms and promote 'sexual responsibility' for lack of a better word. The Pope only supports one of those and specifically, and irresponsibly, campaigns against the other, and thus, is not 'right'.