The IoW was not all powerful- that is a common misconception. It was not the center of this world either. Many of the stories told more about the rest of the world than the IoW. Read the JoJ and other lore for that.
THe IoW only had power that was granted to it by other nations, mostly Demacia and Noxus. If the nations did not support the IoW, then the IoW had little power.
The IoW was not all powerful. The rise of Shurima woud be enormously changing to the power balance of the world. The IoW would not require that Shurima join the IoW. Ionia joined the League to petition for help against Noxus. The IoW did not stop the war between Noxus and Ionia just because there were fights happening.
The IoW's main mission was to prevent wars on the scale of the Rune Wars that had devastated Runeterra. It is wrong to say that they interfered in any conflict whatsoever. It wasn't a nanny organization rushing in and keeping everything frozen. It wasn't a 'Big Brother' organization that knew everything everywhere at all times.
The Kalamanda Incident was a demonstration of how fragile peace actually was. The time freeze was only achieved at enormous cost, not something the IoW could do on a regular basis or over a huge area. Demacia and Noxus came to the brink of war. If they had decided to continue their war, the IoW could not have stopped them.
If the IoW felt like the center of the world, whose fault was that? Not the IoW's, but the writers. Removing the IoW hasn't really changed the status quo. I never felt Bilgewater was under any threat from the Harrowing. It was driven off by people, as I expected. I see little difference between 'IoW helps Bilgewater fight off the Harrowing' and 'Bilgewater fights off the Harrowing.' Either way, the Harrowing is defeated and Bilgewater saved and the status quo remains.
In the lore before, the Harrowing was not driven of by the IoW, but Gangplank and Miss Fortune leading a fleet against it. This was with the IoW around.
For the sake of argument, let's grant the IoW was too powerful. Does that mean it should be reconned out entirely? No. There are spaces between 'Too powerful' and 'Does not exist.' If the IoW was too powerful, it could be changed. Less power given to it by the writers (keep your focus on the writers, for they are the truly all powerful ones). It is lazy thinking to remove things 100% rather than give more nuanced thought to them.
Another thing the writers did that I deplore- getting rid of the IoW without fanfare. When DC rebooted/retconned their universe, they had a huge crossover event with 'Crisis on Infinite Earths.' It was a huge sendoff to the old universe, one that respected the old one and gave us canonical reasons why the old universe was now going to be different. It was not just 'Hey guys we didn't like the old universe, so we got rid of it and here's a new one.'