IANAL, but from what I understand, Alice didn't invalidate software patents. In fact, it's generally agreed that they tried very hard not to rule on software patents. All they did was say that a generic abstract idea (like "escrow") doesn't suddenly turn patentable just because it may run on a computer. You need to have an "inventive concept" to qualify.
Alice didn't invalidate software patents wholesale, but it seems like it killed a lot of the more objectionable ones and collapsed settlement values early in cases.
That particular patent was killed because it was even less innovative, as CompuServe Mall already had shopping carts in a computer before. Unfortunately, it had to go all the way to the court of appeals, and only thanks to Newegg choosing to fight it rather than pay them off: https://arstechnica.com/tech-policy/2013/01/how-newegg-crush...
