Thomas

You can still get the Wired Reflexes perk if you've already told Harkness that he's a synth. Just tell Zimmer that Harkness is the runaway synth he's been looking for and then you eliminate him and his bodyguard. Then you go back to Harkness and he'll tell you that he knows about Zimmer and leaves it at that.

It's the best of both worlds.