The usual argument I see whenever the Konami/Kojima issue comes up, especially with regards to budgets and delays, is that people really want there to be a good guy and a bad guy with somewhere to point "fault" at. But I think there's another way to look at it - at this point their mutual interests were simply not compatible.
For a big game publisher to invest 80 million dollars or more into expanding their biggest action franchise worldwide into a full open world experience, asynchronous online social hooks integrated into the single player, and a separate team based online multiplayer shooter component on every major platform available... is not a bad idea at all. On its own it is neither a bad investment nor is it a poor business decision - provided that said publisher is interested in this sort of business in the future and interested in continuing to invest into this segment to build on it further.
Konami is not that publisher. Ubisoft is. Kojima was just working for the wrong megacorp.
That's how I view it. They both want different things and Konami is going in the direction of low-risk, high return investments in mobile after seeing all the profits there and finding their own success for cheap, but even staying in the console games industry, MGS games are proving to be quite the investment that they might not feel safe taking anymore. It's not like they NEED to do this when they can print money with their slot machines, etc. so if the risk is higher than their other ventures, it's not surprising that they don't care to do it again.
Of course that doesn't mean what they did is right at all and I still don't like them, but 2 parties going in different directions isn't uncommon and we'll never know the full story when it comes to this game.
Just sucks that it has to happen to one of my favorite series in terms of gameplay.
It's not something other publishers dedicated to console and PC games would shy away from, but I understand why Konami might not be too keen on continuing this trend. It'd be a lot more understandable if the whole thing didn't go down the way it did.