Big Boss's story is one filled with morally grey areas was he truly "evil" I personally don't think he was evil I think his way of thinking changed with all the stuff he went through.
At the same time we are in a universe were there are two very powerful secret organisations trying to make huge changes in the world. One trying to create a world state in secret through manipulation and the other trying to a create a place were soldiers are not discarded have a purpose. The latter is understandable think about how many countries have treated their soldiers upon their return home poorly (this is a generalisation I am not saying everybody did this) as an example Vietnam veterans saw a lot of problems back home when they returned from the war by the civilian population.
On top of that there are a lot of soldiers affected by the things they see in war physically / psychologically and there are probably some that aren't but you hear about it quite a bit were retired soldiers or discharged ones have trouble reintegrating into society. You can understand why Big Boss being a Soldier for his entire life and feeling betrayed by nearly everyone around him wants to change things. [Spoiler Below]
Big Boss must have one point realised that him and Zero tore the world apart and that it needed to be corrected its a shame really its just like The Boss a great warrior who loved her country and made the ultimate sacrifice. I like MGSV ending big MGS4 is still the best for me both are powerful the debriefing in the cemetery had me in tears it was that moving.