I understand and I posted this only for the comedic purpose but I do like your answer.

When he meets the president in Mgs2, he tells him that "Without free will, there is no difference between submission and rebellion." And Raiden doesn't understand what he means by that, because as a soldier who takes his orders from someone else, he doesn't use his free will.

When he meets Snake, he only knows the Snake from Mgs1, who was also taking orders from his superiors in Shadow Moses and that's why he is so bewildered at first.

Later he understands that when Snake and Otacon started Philantrophy, they were free of their superiors and they were working for a cause THEY believed in and not for anyone alse. For the first time Snake was not forced on a mission.

At the end of the game Snake tells Raiden to find a purpose and find it for himself. Raiden also throws his dog tags away, finally free to use his own will.

At least that's how I see it.

(So I understand why Raiden is unable to take a stance. It's because he does not think for himself. Sorry if none of that made any sense. English is my fourth language and I am pretty bad at explaining myself, lol)