What a dilemma! I agree that since you asked the mom, it would be preferable to honor her wishes. Yes, black and grey are not traditional baby colors, but hey, who says there is a law that baby quilts must be traditional colors?
When I was pregnant with my first son, my mom wanted to knit me a blanket. She asked me to choose a color and I chose grey. She then proceeded to knit the blanket, complaining, moaning and whining the entire time because I did not choose a proper "baby color". When it was all said and done, the grey turned out beautiful, the blanket was lovely, the baby adored it (and as a 6 year old still does) and everyone was happy. Would that have been the case had she made it a different color? Most likely yes. But she asked me, and I gave her my request. I was thankful as a silly first-time mom fluttering about decorating her first nursery, that she honored my request.
It is always a challenge to work with colors you don't like. I think you can rise to the challenge and create something beautiful (there is appeal in the versatility of a two-sided quilt). If it were me, I'd rather do colors I don't like and have the blanket used than override mom's opinion, pick my own, and have it end up on a shelf. Regardless of color choice, let's hope the new momma has the grace to accept your gift with thanks and no sign of a snit!
Good luck!!