See, nothing she says to Qarr indicates that she's anything but completely loyal to the IFCC ("You don't know what my orders are, Qarr."). The only ambiguity comes in with that last line at the end (and maybe, just maybe, with what she doesn't say), but I think Sabine sees no conflict at all between serving the IFCC and serving Nale, while Qarr does because he doesn't see the whole picture.
What happens if there does become a conflict between serving the IFCC and serving Nale, that's still an open question.