True, but the Dalish have a cultural context here that's hard to ignore. Humans have stolen and destroyed virtually everything the elves have tried to preserve, build and accomplish (since the Veil went up, anyway), and much of that was done in the name of their Maker. You can't just accept the Maker as another god in the pantheon: He doesn't fit in as anything but a supreme creator god, and that position will always put Him above the elven gods, that is, a human god will be always be greater than the elven ones.
She basically calls the elven religion nonsense, and combined with her wanting a Dalish Inquisitor to just "accept another god" it paints a nasty picture. Cassandra doesn't care about the Dalish religion, but she's apparently willing to stomach minor references to it as long they accept that the Maker is number one.
What I imagine would happen would be the elves leaning more towards one of their gods being the "chief deity", as you see in religions that have shifted from polytheistic to a more pseudo-monotheistic, and then that god being seen as akin to the Maker. I do agree there's a lot of cultural context going on there that would make all of it difficult, but that's the only way I could really see it happening. I think there's a lot of potential for religious fusions/divergent sects based on local religions + the dominate religion that hasn't been explored, not just for the elves, but for the dwarves (Andrastrianism that incorporates some of the concepts of the Stone) and the Tal Vashoth (Andrastrianism that takes ideas from the Qun). There's a few things like this already, like the Fereldan song about Andrastre's mabari, lmao, but it would be cool to see it explored more. Religions that are fundamentally incompatible philosophically tend to have conflict, yes, but they also tend to hybridize sometimes especially if one is colonizing the other (as Andrastrianism is doing).
With Cass, I found that remark incredibly frustrating. I felt like my Inquisitor's interactions with Cass were ones of respectful difference for most of the game and it was really nice (I didn't get the "accept another god" dialogue with her), but that remark left me feeling like Cass only respected my Inquisitor's faith because she had to respect her, not that she had any actual respect for other people's faiths.