The key here is that she hasn't yet seen reason to change that point of view. While the treatment of damane is shocking, I look at the AS whom she has seen, and none of them act like anything other than children at best. No wonder she considers them dangerous, considering they wield such power (as for the Oaths, the Tower controls politics easily enough with them in place to discount them).

Tuon's priorities (unlike most other characters) are in the right order. Her people, whom she is responsible for and who look to her, come first. She is aware of the paradox of enslaving channelers, but there is no pragmatic solution to this at this time which won't hurt her people and remove order.

There are definitely flaws in the Seanchan Empire and in her leadership, but I think those come from factors outside of her control. Her decisions have made sense, and she is dealing with politics and risks far deeper than any other character aside from Rand. Egwene's struggle over a few dim-witted AS in the tower is nothing compared to maintaining order and military strength in half of Randland. Even if they never join with Rand, there's no chance they will join the Shadow under her leadership.