I don't believe for a second that the majority of Apollo users wouldn't have used reddit if Apollo didn't exist. The value that Apollo provided was ad-free experience (which obviously is better than having ads) and a better UI. Apollo did not bring many *new* users to Reddit so arguably, Apollo is practically useless to Reddit in terms of increasing "popularity".
That's fair to believe but you have zero evidence supporting any of your claims.
Reddit itself did not ban third-party applications altogether, which means they do recognize some value in them that they provide to the platform. They own the platform and they could have simply banned them instead of making the API pay-per-use for them. This was Reddit's own statement on the matter, emphasis mine:
We’re committed to fostering a safe and responsible developer ecosystem around Reddit — developers and third-party apps can make Reddit better and do so in a sustainable and mutually-beneficial partnership, while also keeping our users and data safe.
In general, I still don't understand all of this emotionally charged reactions, with people angry on one side, gloating on other side... both Reddit and Apollo were and are making ultimately business decisions.
Apollo was using APIs provided by Reddit and never stole, hacked, misused or freeloaded off anything from Reddit as far as I understand. Reddit provided the API free of charge to allow a third-party ecosystem they did benefit from by making Reddit better, as they themselves stated. This is a value exchange, even if no money is involved.
Reddit owns the platform, they can change the rule at any time. Now Reddit decided to set a price for the API and some API users consider the new value proposition very much inadequate, which is perfectly fair on their side just as it's fair for Reddit to stick to the price they want. If the price is too high, few will buy but maybe that's Reddit's goal after all...
Neither side is deserving of any "fanboyism" IMHO.