True. Maybe they were just so stunned by everything.

On the other hand, Lucius gets 100,000 gold and Potter in his debt, which apparently gives him some kind of control. And maybe he realized Hermione wasn't the actual killer, but couldn't back down at that point because he'd lose face. So it's not like he ends up with a bad deal.

Alternatively, if he thinks Harry is his real enemy and Hermione just a minion, maybe having Harry in his debt is just as good as putting Hermione in the clank, according to his utility function.