Being really strong isn't the Harbinger's problem, being boring is.
As Megas said, the reaper boat loadout is just so overwhelmingly better than the rest. With expanded missile racks, that's potentially 10 destroyed enemy ships from the get go in any battle. I single handedly stopped raids and took down battle stations with the simple QD/Torpedo combo, and it is not only fast, it's also easy to do. As someone said on the discord at some point, once you get a Harbinger, the game change from a challenge to a grind. You repeat the same routine of assassinating the flagship over and over again, all with little risk.
Of course, i could try something else. A Blaster/Phase lance/Ion pulser variant isn't bad at all, but is lightyears below a reaper build when it comes to burst damage, and if you're planning to use this loadout for prolonged engagements, delicate machinery and time dilatation will wreck your CR, limiting your influence on the battlefield.
Quantum Disruptor is the problem. It wasn't that bad with the Afflictor thanks to the very limited ammo from small reaper launchers. Fielding an assassin Afflictor was viable, but risky when you can screw up your single (two) chances. But with the Harbinger? A bit too easy, and it get boring quick.