What the conspiracy theorists overlook is the point that Povol has made on several occasions; ie that Rossi was simply not fast enough late season. Any conspiracy could easily have been subverted simply by Rossi being fast enough to get in front of MM or Lorenzo at PI and Sepang and stay there, or by him being faster than Pedrosa at several races or Iannone at PI. I suppose he might have had a different approach at Valencia had the back of the grid penalty not totally removed the possibility of him finishing better than 4th on his own merits, but as others have said it seems unlikely he would have had the pace to finish any better than that anyway.
The points that Kropotkin made which are incontrovertible imo is that the Spanish conspiracy theory involving Dorna is ridiculous, it was overwhelmingly in their interest for Rossi to win the title, and that there is not much way around whoever is on Race Direction or any equivalent being in Dorna's employ given they own the sport. From my point of view at least the FIM are at some remove and know something about the sport (as opposed to Dorna), but as I said I am inclined to believe David that the current members of RD are honest men. My general opinion of Dorna is that they are not infrequently incompetent and that Carmelo tries to imitate F1 too much apparently not realising bike racing is a different sport, but that they do not contrive actual race results.
Conspiracy theories are usually suspect by their nature in any case, but given at least one conspiracy held by many, ie that Dorna because they are Spanish conspired to help a Spanish rider win the title , is patently insane as David says, surely this hardly lends credence to other conspiracy theories advanced by the same people. I certainly think that the penalty Rossi received was the minimum he could have been given, and perhaps RD could have been influenced by factors such as Rossi's stature in the sport, a desire not to completely decide the championship off the track and make the last round a dead rubber, or even some anticipation of the criticism they would receive, but in the end they did give him a penalty, and a back of the grid penalty in general terms is a severe penalty if not as severe as a disqualification.
As you say few minds will change now, but this all started with the supposed conspiracy at PI, which remains ridiculous imo, given Dani Pedrosa was 5 seconds down the road from the supposedly sandbagging MM on the same bike despite having competitive or better pace than MM at other late season races, even apart from that sandbagger actually winning the race.