Well this is it, really. If your reason for supporting abortion is based on the autonomy of the pregnant woman, then you have no logical reason to object to sex selection as a valid reason the same as any other.
Like I say, I see the conflict, because abortion is considered a women's rights issue, and sex selection to abort girls goes against that point. But if the basis of the pro-choice argument is autonomy, then on what basis are we deciding which autonomous choices are unacceptable?
The decision to terminate a girl is rooted in misogyny, of course, and dealing with the misogynistic culture is probably important there (good luck with that, btw). But plenty of women terminate with very mixed up motivations. A child would make an education difficult. A child would complicate a relationship. A child would be financially problematic.
All of those motivations are connected to other things which are potentially misogynistic, and you could say that the important thing is to deal with the structural issues that mean the woman feels abortion is the best choice.
But you've already conceded the point that personal autonomy is the reason women should be able to have abortions. You don't have anywhere to go to say some abortions are acceptable, and some aren't.
Either abortion is about a woman's choice to have control over whether she gestates a baby or it isn't.