This would only be true if throwing was a major gameplay mechanic you do constantly (which I don't think is really the case for this game), and the timing wasn't tuned to be reasonable (a setting in the options menu to manually tweak it would help with this).
And it wouldn't have to be a hold input specifically. Maybe a charge-and-release input. so if you tap left click you basically just drop the item, but if you hold it down and release you throw it depending on how long you charged it. Something like that.
Or scrap the hold input idea and just make left click throw like in HL2.
EDIT: Thinking about it, just making left click throw physics objects would make things a lot simpler and straightforward overall, and not require the addition of a whole new game setting.