Apologies for being a bit brief. I'm rarely home these days so I can't always post from a computer and make lengthy replies. Allow me to explain. Conan basically only knows two things... That 1) His phone was different and it was likely Akai whose prints that they were after and 2) that Rikumichi's prints was also on the phone and he is confirmed dead and that there is a possibility that the body was switched. That said, there is no reason for Conan to make that leap in deduction without proof. Akai never trusted Conan enough to tell him anything, especially not when he didn't even tell his partner what he was planning. So Conan has no reason to believe that Akai is alive, which is why it is "wild speculation." Unless Gosho reveals that Akai made the plan with Conan as a back-up to get Kir back in, there is no reason to assume that he knew anything about what was happening. Is that possible? Yes, but it is a bit of a leap, imo.
This is opposed to the clear difference in the body positioning and lack of blood trail in the frames in the manga. Gosho himself usually takes care of frames like that, so the possibilities of it being a mistake by one of his assistants is slim to none. So that is a far more telling and compelling evidence than a reaction from someone who may have only figured that the FBI agents knew what they were doing and were prepared to die and chose not to worry about it. Not to mention that he never really made a strong connection to the FBI like he did with the MPD. I think if he heard that someone in the MPD died, there would be a much bigger reaction, despite knowledge of a plan to keep the said MPD officer alive, because he knows that there is always the possibility of something going wrong. So believing everything went totally to plan, ESPECIALLY with the BO who has already bested him on multiple occasions, would be frankly stupid of him.
That said, the rest of what you said is actually a part of the set of deductions that have been posted here and in the wiki as well as on DCTP that is essentially accepted as why Akai is alive.