Renewal and in-game purchases came as a response to an already declining popularity. I don't think the author of this article is qualified to say if these changes ended up being beneficial for Gravity and their publishers. The bot problem is likely a product of cuts in staff, again as a result of declining popularity. Also I don't think Gate of the World and Legend of the Second actually were that bad. They just weren't what the audience of Ragnarok Online wanted, and by the time they got them out the market was already over-saturated. In summary I don't think any of these were direct reasons for why the game isn't as popular anymore. More likely it's because it's an old game. People grow up and you can only keep it interesting for so long.
However the point about publishers is fair enough. I've heard that the licensing model may have difficulties. The last section also gets into what I believe, if anything, is the reason why there's been a few bumps in the road for Ragnarok. Gravity wasn't an AAA game developer when they started on Ragnarok Online. In fact they weren't even Gravity Co. Ltd. until mid development of Arcturus, which they developed in cooperation with Sonnori Entertainment. Before this they were Team Gravity, a team of indie game developers who made DOS games in collaboration with other minor studios. Arcturus became a success in the Asian market, and they managed to raise about $700,000 in paid-in capital for their new project. At this point they reused the development tools and source code from Arcturus for the game client, and brokered a deal to create a game based on the popular Ragnarok comic. Saying that Gravity at this point were close to bankruptcy is misleading. They were very much a start-up company and needed investors to get their first big project out there. A few years later they had one of the most popular MMOs in the world. How's that for failure?