The rent-a-goons scandal (which it certainly was) could not have been an event organized by anyone with any semblance of a brain- it made bad PR, a legal mess, and other issues. While there are definitively some members of the RNC with questionable intellects, there are others that would recognize that as being a truly unfortunate outcome- thus it was almost certainly the actions of a local 'overachiever' rather than a conspiracy.
As for the rest, I don't believe in the vote-flipping theories, and the 'outright cheating' in the conventions has been a common accusation of both sides against each other (Santorum's group recently condemned Paul's group of it in Iowa, for instance). The main reason being that the delegation process has informally changed throughout the years, and some people are playing with the informal rules while others follow the formal rules. I fully expect this discrepancies to be solved within the next ten years and the delegate convention process to be changed dramatically.
That being said the Republican Party doesn't hate you- it wants your votes and has no problem with people that are libertarian within its party (Rand Paul for instance). It certainly doesn't trust you guys, however, and that distrust will deepen into outright rejection if this lawsuit gets a lot of media coverage or goes viral (otherwise everyone will just forget this ever happened, even if it does go to court). And while you guys think time is on your side, they think the same: with Ron Paul retiring there is no obvious leader of the movement, and movements without leaders tend to fall apart given time.