Because you want to teach them a lesson, not put them out of business.
A fine is meant to deter as well as punish. If the fine is too small, it won't deter. And certainly if less than the profits earned, it can't punish, nor deter.
Losing $650 million is perhaps not quite as compelling a story as losing billions, or a smoking hole where a company used to be (as in Enron and Arthur Andersen). But it's a pretty big chunk of change. I have no experience making such arguments, but it seems plausible that it will be remembered for a while at Equifax and their competitors, at least?
I'm doubtful that people respond to such incentives rationally. It probably has more to do with how well the storyteller tells the story. And whether the thing they're selling actually works well for improving security seems pretty hit-and-miss, too.
It seems less scofflaw companies aren't offered the chance to serve the same markets because criminal companies are let off too lightly.
Primarily, I want my justice system to administer justice.