If she had stepped down before 2016, Obama would have been able to appoint another liberal judge to replace her, and the political balance of the court would have remained unchanged. Instead, she died in 2020 and Trump replaced her with a far more conservative judge, which is indirectly one of the reasons why Roe v Wade was just overturned.

Of course, it must be remembered that almost no-one actually expected Trump to win 2016. So perhaps she didn't feel like there was actually much risk of her being replaced by a conservative, so it was safe to stay on.