No, Harbinger does not need nerfs if Quantum Disruptor gets better. Harbinger with old QD was only overpowered with Reapers. After Harbinger lost Synergy mounts, it became inferior to Afflictor ever since, and it did not punch much above its weight, if at all, like Afflictor and Doom could. QD being used against you could be annoying, but just that, annoying.
Without QD, Harbinger gets shot at every time it decloaks to attack, not unlike a no-shield armor tank like Vanguard. Right now, the only recourse is it use Ion Pulsers and maybe shut down the enemy before it shoots back much. Normal Phase Lances are not an option because its beam reach is longer than its system. (HSA Lances have too short range.) Other weapons do not stun the enemy, and Harbinger takes unavoidable damage trading shots, just like Vanguard. If Harbinger had Rugged Construction like Gremlin or Grendel, trading shots like this would be okay, but it does not.
With cloak delays and most weapon reloads, Phase Anchor is mostly useful for death prevention and avoiding d-mods on phase ships. With weapons that reload faster than AMBs (which is nearly all of them), after ship decloaks and attack, I wait too long (at least without elite Field Modulation) before my ship can cloak again, which is too late for the faster reload time to be of much use. If I want to use AMBs, Afflictor uses them better than Harbinger can. Phase Anchor is great on Ziggurat though, because it has Experimental Phase Coils to mostly eliminate the cloak delay, which works great for needlers and tachyon lances without cloaking delay getting in the way.
These aren't faults in the Harbinger or Quantum Disruptor, these are faults with the phase system itself. Every phase ship is designed from the ground up so that it takes damage on leaving phase. Your needlers on the Ziggurat? Wasted because the firing time is longer than even standard phase cooldown. It's still taking damage. Level up your game and scalp kinetic blasters from the Lion's Guard.
And you don't need ion pulsers to disable return fire. Elite Target Analysis will do just fine. I run a Grendel and it increases survivability by quite a lot, more than field modulation.
But phase ships are made to die. You spend hullpoints like you do flux and choose your fights for maximum benefit. The hard deceleration after leaving phase guarantees it. The cooldown doesn't even matter by comparison. It's like phase ships get hit with Interdictor Array every time after leaving phase. It sucks, but the ships are workable.
I, too, would like phase ships to be redesigned, and even if they had everything I wanted, Quantum Disruptor as it stands would be bad. A free shot you can pull off over and over again with the only cost being time is just stale. It's not powerful, it's just a comparison of your PPT against the enemy fleet.
Worst of all, you're still getting shot every time you leave phase with QD. You're not going to time it right, it's not going to last long enough for a full volley, and you were already taking fire before you unphased. It just doesn't do what you claim at all.
Frankly, just fitting the Harbinger with Burn Drive would make it a much more competitive ship.
Movement Disruption at a glance looked more like immobilization. So, it looks like you want Harbinger to drop space grease under the target and have it slide wherever. With constantly backpedaling enemies facing their target, it would probably function like an awkward tractor beam. If it ends up working like a tractor beam (because of everyone points at their enemies), then make it a tractor beam, but it would look better if a capital ship sucked in a small ship than the reverse.
Nope. Eagle is retreating, you use the system, and it backs off out of range. If it tries to follow you and fire while keeping out of your range, use the system, and it accelerates back into your range for another round. A hound starts running to your back side, you use the system, and it just burns away away long enough for you to turn around.