I can not comment about behind the scenes meetings of covert ops to go in and recon the crash site that was found months later, but little facts in the article that do not jive make me suspicious that this story is, at the very least, being sensationalized for the purpose of selling newspapers or books.
Nothing in the article was sensationalized. It was determined to be air wing policy to turn off the ELT, against the advice of SPEAR--the Navy's premier operational intelligence unit. The radios VFA-81 carried on the first strike were new; VFA-83 didn't carry that model radio on the same strike.
Spike's case is unique in the history of the U.S. military in that he is the first and only person to be officially listed as MIA from any war. The behind the scenes investigation into his whereabouts is one of most significant as well. There is much that the fog of war taught us from January 17, 1991, and it continues to unfold around this particular case.