It looks to me like her mom is supposed to be purple+white while her dad is midnight blue. Twilight Sparkle's not blue or white at all, but she does have a combination of light purple (like her mom's mane) and deep purple (like her dad's deep blue). The pink is still very different, but maybe that bright coloring is just a sign that she's youthful. It sort of resembles hair highlights, which I would associate with young, vivacious people (that sentence must make me sound fifty years older than I am).
Purple eyes aren't exactly a midpoint between blue and yellow, though. I think at that point, the designers were just having fun with eye colors. They probably didn't think "what eye colors would Twilight Sparkle's parents have," but "what colors would these two ponies have (with no reference to Twilight Sparkle)." So they looked at each design separately and gave them the eye colors that looked best on them individually.
You could also theorize that one of her grandparents had pink hair and purple eyes.
I don't think the designers wanted viewers to take the hereditary coloring TOO literally, like scientifically literally.
...Wow, that was a long post