The damage changing the tyre did to ducati and hence stoner may have been tangential to decisions made for other reasons, but I don't think it is unreasonable to suspect that reducing stoner's and/or ducati's perceived advantage was involved; I refer to your tyre conspiracy of 2008 rather than the control tyre which I don't think was aimed against stoner or ducati, but rather at closer racing (theoretically) and lowering costs as was said , for dorna at least since supplying the tyres free to satellite teams was part of the deal.
I think the debate hinges on Rossi's switch to Bridgestone. Sadly, the details of Rossi's switch will probably never be known, nor will the cause of the switch be traced to a single conclusive event.
If Rossi demanded Bridgestone tires to increase his income earning potential following the tax scandal with Italian authorities, I'd say that Casey Stoner was deliberately targeted during the emergency meetings of 2008 b/c Rossi's sole motivation is gaining a competitive advantage on Rossi. However, I think the tire meetings could have been influenced by equally powerful, yet less-biased, demands from other parties. The FIM and Dorna may have had insurance problems regarding the circuit homologation safety specifications, which were rendered inadequate by the rapid increase of cornering speeds. It is also possible that Bridgestone may have done an about face. Prior to 2008, the company was outspoken about their ambitions to showcase technology by beating Valentino Rossi. However, I believe Bridgestone could have sought Rossi's services as compensation for sacrificing the technologies they had developed for 800cc competition.
I suppose that Rossi's competitive nature, Bridgestone's contingency plans, safety concerns, and Dorna's commercial ambitions probably all contributed to the 2007 tire meetings and Rossi's switch to Bridgestone. If the tire meetings were caused by multiple factions with multiple agendas it would certainly explain why the GPC are nearly as divided on the issue as PS members. However, I have noticed that the line of demarcation on this board tends to depend on pro-Stoner or anti-Stoner factions. The GPC has much stranger bedfellows regarding the tire issue.