Generally, the manga is not considered to be canon, so I wouldn't make the focal point of your argument around the manga.
More importantly, though, it's highly unlikely that Agahnim is Sheikah, primarily because the notion of the Sheikah did not exist at the time ALttP was being developed. It is possible that Nintendo based the Sheikah symbol off of the one seen on Agahnim's robes as an homage. It is also unlikely that Agahnim is of Sheikah ancestry, because the Sheikah had more or less been wiped out by the time of the events of OoT.
Lastly, I'm not sure if you've played ALttP, but it is revealed in the game that revenge is not his primary incentive for usurping the throne. I'll try not to spoil any more of the game, so I'll just close on saying that, to the best of my knowledge, the game does not have any evidence to support Agahnim being a Sheikah.