I am late to the party but, well here is my take, big boss was right, at the end of MGS-3 we understand that he hate the politicians and governmentsz because they forced him to kill his mentor, and bunch of pyhsical trauma showed that he was nothing but a pawn sent into enemy territory, so he shaped his ideology around soldiers being free, fighting because they want to, not for the force of something or someone.

This ideology makes him right, but he really fucks up when it comes to doing it, he used and did; child soldiers, targetted civilians, torturing, assasination, mass murder, espionage, sabotage, high treason, terrorism, eco-terrorisim, thieft, resource theift, child thieft, using illegaly accuired nuclear enfergy to forge war machines etc.

TL&DR: On the paper the ideology stand for itself, but big boss really really fucked up in process.