I struggle with this theory because some had to have assigned jobs to these deities. Someone must have said Mythal was in charge of Justice, Fen Harel in charge of rebellion, and Elgarnan in charge of the sun.
Who assigned these gods their portfolios?
Their worshipers.
There's a lot of assumptions in the OP,
Your first assumption is that the Maker exists at all, and isn't just a hopeful figment of people's imagination. In a world where the gods that we know exist (elven) kept slaves and sounded like right bastards, it isn't entirely out of the question to assume that some people might prefer to believe in a god that didn't keep slaves or even interact with the world at all - even if that god had to be made up.
Now, if the Maker does exist, why is it assumed he is good, or cares about the quality of life in Thedas? Before he created Thedas, he apparently had already made spirits, angelic beings with purity of purpose. There was no pain, and since we know that spirits only become demons if corrupted from their purpose (by mortals), there was no sin. If the Maker wanted a perfectly good and pure world, we can assume he would have stopped at spirits and wouldn't have made mortals at all.
If we believe the myths that he created mortals because he wanted more change and meaning, then we also have to assume that he introduced evil into the world to act as a counter point to the pure virtue that already existed thanks to the Fade. Philosophically, the presence and persistence of evil is what gives good and virtue meaning. Without conflict, virtue has no meaning, it simply exists. It is only within a world of uncertainty, chaos, filled with evil, that purity, virtue, and goodness mean something.
Choice, motivation and uncertainty is what defines mortals and Thedas when compared to the spirits and Fade. If the Maker directly intercedes, shows himself, and picks a side, then it completely negates that meaning, and ultimately negates the purpose of his creation. If people are good because they know, without a doubt, that a higher power wants them to be, then it ceases to be a choice.
It's my belief that if the Maker exists, he didn't create mortals - the Maker simply gave spirits the ability to make decisions, to choose. As long as people can continue to make choices, of their own free will, his creation has meaning.
And if Thedas is to be destroyed, it will be at the hands of the mortals, either through action or inaction. But if it is to be saved, it will also be at the hands of the mortals. Either way, there is true meaning and real choice, regardless of how many suffer.