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The Sisterhood have never been shown to be antagonistic towards the Doctor, though they have occasionally seemed irritated by him & once -- briefly -- suspected him of trying to steal from them ("The Brain of Morbius"). They have often been sympathetic to him & have sometimes given him their active assistance (in "The Night of the Doctor", for example).

Karn was originally a Gallifreyan colony & the Sisterhood has normally had an amicable -- though somewhat distant -- relationship with the Time Lords. They supply the Elixir of Life to the Time Lords.

From what little we saw of them during the Last Great Time War, they appeared to share the Doctor's attitudes to the war & to the Time Lords' conduct of it. In "Hell Bent", when Ohila told Rassilon that the Doctor didn't blame Gallifrey for the horrors of the war but blamed only Rassilon himself, she made it clear that she agreed with the Doctor & was herself antagonistic towards Rassilon.

The Sisterhood opposed the Time Lord criminal Morbius vigorously & repeatedly, even to the extent of aiding a military alliance against him. They put Morbius on trial & Maren, their leader at the time, attended his execution ("Warmonger" (novel), "The Vengeance of Morbius" (audio story), "The Brain of Morbius").