You can now set on a price book whether you would like any invoice line-level discounts to be shown on the invoice PDF. Simply go to Products -> Pricing -> Price books -> Click 'Edit basic details' next to the relevant price book, then tick 'Hide discounts on invoices using this price book from being displayed on the invoice PDF'. After enabling this setting, any orders created with this price book will then have their invoice line-level discounts hidden on the PDF.

Especially useful when a price book has a negative discount that increases the price!