"Yeah it's unfortunate, it's messy, I wish it hadn't have got that messy and in hindsight I think there were probably steps that were missed that wouldn't have made it that messy," McIlroy told BBC Sport NI at the JP McManus Pro-Am.
"But I said this back at the very start in 2020, I think in the long term it will make the game better because I think it will force the tours to adapt and change and make the product better, and focus on maybe the fan engagement side of things and focus on maybe some stuff that they've been neglecting over the years.
"I think in the long term it will sort itself out, as everything else does, it will, and I think ultimately it will make the game, and the game of professional golf, a better place.
"But right now there's just this disruption happening and with disruption comes change and forced change, and I think this has just forced the tours' hands a little bit and they have to adapt and change, and that's what they'll have to try and do."
With the PGA TOUR suspending rebels indefinitely and the DP World Tour forced to suspend its ban on the likes of Ian Poulter and others playing in this week's Scottish Open, McIlroy reckons there needs to be dialogue between all the parties.
"I think so," he said. "I think that needs to happen. Look, there's so much chat about where the money's coming from and Saudi and everything else, look they sponsor so many other things and they're all over sport.
"Aramco are big sponsors of Formula One, the Aramco Ladies Series in golf, which has actually been really good for the Ladies in terms of big prize funds and so on, so I understand people's reservations with everything.
"But at the same time, if these people are serious about investing billions of dollars into golf, I think ultimately that's a good thing.
"But it has to be done the right way and I think if they were to invest, having it be invested inside the existing structures.
"And I think that's the thing I have tried to advocate for the last few months, I think at this point if people are wanting to spend that much money into golf that's wonderful, I just wish that we could have spent that much money within the structure that has existed for many decades in golf instead of being a big disruptor.
"But at the end of the day, as I said it will sort itself out and everyone has to pivot and change and try to adapt and be better, and hopefully we get to that stage.
"Right now it's sort of messy and all the narrative isn't good, it's splitting the game instead of everyone coming together and I think everyone has to try and come together a little bit more."
As for negative of comments directed towards "defectors" on social media, including death threats to Graeme McDowell, he said: "I think defection is a strong word. I understand why guys have went, especially the guys that are sort of in the latter stages of their career and if I was in their position, I'd serious have to think about doing the same thing.
"It's the younger guys to me that I find hard to understand because they're losing years of their competitive career for monetary reasons. We all make decisions for different purpose. That's fine. It's different to what I'd do.
"Is there resentment? I played in Ryder Cup teams with these guys. Is there a difference of opinion? Yes. There is a difference of opinion and I would have done things differently.
"I think at this stage if you go and play on a different Tour, then go and play on a different Tour. I think having your cake and eating is the resentment that's within the membership.
"Because there's only 48 players on this Tour, so not everyone's going to get an opportunity to go and play. You're leaving all your peers behind to go and make money, which is fine.
"Just go over there, don't try and come back and play over here again. That's the tricky part and that's where the resentment is coming from. For me, I don't resent anyone. These guys are my friends, regardless of the decisions they make."