Reapers in Freelancer? They're here already. Sure, they look kind of primitive and basic, but that's what happens when you break Zoners down to make them.
Besides, I'm sure Akura is right about the single player campaign being better for Freelancer's humanity if the Order hadn't interfered. I mean, it's not like anyone likes that pesky life thing. I'm sure they'd all have appreciated having humanity tear itself apart at the behest of shape-shifting parasites, followed by a crippling final extermination from a checkmate alien invasion.:P
Still, I understand where you're coming from on the metaissue of moral highground. It would be like comparing them to the Native Americans of old. If the Natives scalped people. While they were alive. Then took over their brains. And made white people kill each other via mind control. And the settlers didn't know the Natives were there, until they wandered into the Black Mountains and cracked open a burial ground where they all happened to be taking a nap.