Don't the Zexen Knights mention something about God as an entity at one point? Also there's the Grasslands spirit worship religion, the Falenan worship of solar cycles and river currents, Eresh is said to be wearing the robes of the clergy of Nagarea, whoever or whatever that is is yet to be revealed (right?) Harmonia worships Hikusaak as a god-king, and Ancient Armes were said to be sun worshipers as well, though the exact nature of their religion is left undefined. My point being that it's incorrect to say that the runes are the gods, the runes are certainly used as "proof of divinity" but they themselves are not the objects of said worship. It would be like saying the Holy Grail was a god, it has divine properties within Christian myth but the tenants of Christianity don't fall apart without it's presence
Since in the real world Gods are generally used to explain things which science can not, things that we still consider magical based on the fact that we don't understand how they happen, and in the suikoden world the True Runes are responsible for all things magical and hold sway over all things that occur in the world from the elements to the sun rising and setting to life and death. Also I'm pretty sure that Falena worshiped the first Queen of Falena as a God because she cam down off the mountain with the Sun Rune, however we find out later that the nation before Falena also possessed the Sun Rune so she was not a God just the bearer of the Rune the lead the nation. Hikusaak is also worshiped as a God-king because he is the bearer of the Circle Rune. I'm not sure enough about the Zexen God's or their mythology but I would wager that if they're not linked to the True Runes they're similar to Roman and Greek Gods serving the same purposes the True Runes serve and as Vextor said Luc refers to them as false which would lead me to believe they are.
My very long winded point is it wouldn't be any more incorrect to think of the True Runes as Gods then it is to think of anything or anyone else in the real world or the suikoworld as Gods.