There have been issues surrounding Konami and their relationship with Hideo Kojima for quite some time. The tension was palpable even as it began, but has unfortunately resulted in the somber split between the two parties. But the reasons why this bad blood came to be is quite shocking, perhaps even inhumane.
The Nikkei reports that the feud is almost entirely based around Metal Gear Solid V and it's budget.
The report from Nikkei (which is behind a pay wall and is of course in Japanese) was very revealing. The budget seems to have been the primary reason for the disdain between the two. At one point it seems that the entire budget for Metal Gear Solid V ended up reaching around $80 million. Kojima also continually asked for more money. Konami had apparently noticed that Dragon Collection, a mobile game, was able to be completed for under $1 million and was a great success. That inference (though not entirely relevant or logical) was the primary reason behind Konami's dismissal of Hideo Kojima.
What's more is that due to the increasing budgetary demands of Metal Gear Solid V, other games they had planned had to be put on hold in order to make room for this most expensive project. Suikoden and Tokimeki Memorial specifically were put on hold until further notice. High budgets and spending as much money as Konami did for MGS V look to be the grounds for shifting their strategy to a primarily mobile and remake strategy.
They also elucidate on poor working conditions rampant at Konami and Kojima Productions. Communication with the outside world while at work was limited to a high degree. Randomized email addresses are assigned to employees and changed often to discourage regular communication.
All manner of breaks from work are highly regulated, but more than that (because that's common throughout the world) should you be late coming back to work, you might be publicly ridiculed for that lateness. Employees are reportedly monitored beyond what might be considered acceptable in the West. And if their performance falls below the expected level, even as a graphics artist or programmer, they might be forced to perform assembly line work, security, or even cleaning duties.
Perhaps the most oppressive act is that of being disciplined for merely liking Facebook posts of former employees, especially should they have received new employment elsewhere.
Some level of employee performance and monitoring is generally expected in nearly any occupation, but it seems that Konami's internal processes took things perhaps a little too far. In any case, it clearly didn't have quite the effect as intended, otherwise they might still be happily pursuing bigger and better projects. Instead, Kojima Productions has been disbanded and Konami has shifted their strategy drastically.