Xil's dislike against Vivienne goes beyond Vivienne's stance on the mage rebellion: Xil's dislike is also based on an expectation of what Vivienne should be as a female mage.
Xil has consistently expressed far less antagonism against people uninterested in the mage rebellion, and even people actively opposed to said rebellion, than she has to someone who defies her belief of what a female mage should believe.
So Xil favors characters who want to take down a system she finds to be morally and ethically reprehensible, because she thinks mages will be mentally, emotionally, and physically better without being subjugated under it, while she dislikes characters who support this system.
I'm not seeing the issue. Vivienne may very well surprise us all and show us layers that we didn't expect, but I don't see the issue with Xil disliking Vivienne do far.
And yet remained extremely ignorant.
Hawke is certainly ignorant about the Eluvians, but he's a human who knows virtually nothing about the plight of the People. Merrill, in contrast, says the Eluvians can help the People. She's performed extensive research. She's more informed about their potential than anyone else in the narrative of Kirkwall.