There are several ways that this could have gone if you ask me.
To be perfectly honest I am still not convinced that Venom is who David really killed at Outer Heaven 1. One of the reasons for this is that George Kasler actually tells David during MG2 that Big Boss died at Outer Heaven. And that BB was later rebuilt by Dr Madnar as part of the Snatcher Project on the orders of an ''eastern despot'', now part man, part machine. With him breaking loose eventually..
MGSV states that Big Boss' ''phantom'' was killed at Outer Heaven, they never explicitly say that it's Venom. And Venom.. I'm still not buying him as a random medic that just happened to get caught in that helicopter crash with Big Boss.
But back on topic, even disregarding all of that stuff and going with the mainstream interpretation.. one thing we have to consider is WHEN did Zero actually lose control over the organisation? When did he, as concious person stop making the decisions and when did the emotionless AI's take control?
And how can we be so sure that Zero wouldn't actually kill Big Boss if he could not control him? Maybe he was pushed to his limit. They more or less went to war with eachother at some point and who knows how far Zero was prepared to go to subdue Big Boss. He wanted him to be his posterboy, an icon.. but what if your posterboy hates everything you stand for and refuses to act as your pawn? If bringing him into the fold was not an option and if Big Boss was taking direct action against the Patriots by creating his own military nation and working against them? Big Boss hated what Zero did with the Les Enfants Terribles project, according to Eva and this is what created the largest rift between them.
Maybe them keeping Big Boss alive after the fact was Zero showing some remorse or seizing the oppertunity to keep his body for future research? Big Boss' body was extremly valuble and was used to create the Next Generation Special forces, atleast three clones and who knows what else. There's so many possible ways it could have gone down..