I completely disagree. AI never acknowledged anything when Rueben won over Clay and I think that caused much more of an uproar than JOH not beating Kelly Monaco. The only thing they ever say with any of their "controversies" is "go over to the phone and vote".
I'll take your word on AI because I've never watched that show (or any other reality show). But I think you can distinguish that situation from the DWTS mess because in the latter case, I don't think the phone-in results were what pissed most people off -- it was the judges' scoring on the last dance. Again, rightly or wrongly, people perceived that as the judges throwing the contest.
But, as was posted earlier today, that's the way it is done in Australia. It's not as thought it were planned in some way to "rig" the show. I don't see how that de-legitimizes the results.
That may be how it's done in Oz, and personally I don't have a problem with it since it allows a couple to have an off week and still come back with a strong performance. But we're talking about perceptions, which don't always follow logic. Most TV viewers don't have a clue how it was done in other countries. I think tinkering with the phone voting is an easy way for ABC to say to those put off by the results "hey, we're trying!" Obviously, ABC may well disagree and decide to do nothing, but I do think that's all John was saying about making the show "great again." Not that it was "great" when he was winning and "not great" when he wasn't, but that some viewers believe they've seen the Wizard of Oz behind the curtain and that ABC could take steps to tweak the show to try to recapture some of the legitimacy it's lost, and the voting is an obvious place to start since ABC can't very well say "the judging sucked" or "yeah, you're right, we rigged it but we promise not to do it again."
Everyone knew the rules up front. They might be stupid and confusing, but they were well known.
I think you're overestimating the average viewer. As was noted above, the % of viewers online or paying close enough attention to what Tom B was saying is probably tiny compared to the overall viewership.