Although there are plenty of names I sorta like that I ignore because of a painful personal association, I wouldn't give up a name I had loved since I was 5, particularly one with a family connection, because of a mean girl from school. Of course, I say this from the perspective of one who left school a long time ago. In 20, 30, 40+ years, you won't care about Mean Samantha anymore, if you ever think about her at all. If you use Samantha for a daughter, she will be the only Samantha association that matters to you.
If I were you, I'd steer clear of Lynnette. Not because of Mean Samantha, but rather because it's boring and dated. If you want to honor your friend, why not Samantha Haylee? Or mix'n'match letters and go with Samantha Leanne, Samantha Annalee, Samantha Leah, or Samantha Haya. You could probably make hundreds of names out of the elements Hay, Lee, Lynn, and Anna, especially if you use Anna's many variations.