Harry's not to blame, but the person Lucius believes is posing as Harry might well be.

From Lucius's perspective it must seem more likely that Hermione is a cat's paw than that she's actually strong enough to beat Draco fairly. Plus, having a Muggleborn arrested for the attempted murder of another student hurts Dumbledore as well. It would be far from unreasonable for Lucius to leap to conclusions at this point.