While historically Japan was more leniant with regards to homosexuality, it was homosexuality within VERY strict rules - like, you screwed with your samurai teacher as part of your learning and then you went off and married a nice girl for teh babiez.

Also, how would this be any different from those arguments that say yaoi/shonen-ai increases awareness about gay rights?

The different would be that Naruto ISN'T gay erotica - it would be a shonen manga with gay characters, which, as someone in the comments can have a hugely positive impact.