Instead of taking away damage from weapons that people already have, why not make other weapons more powerful to balance it out as you say?
I've spoken against this logic before, but it's been a while so I'll give the argument stains once more.
If you balance the weapons by constantly adding to weapons, you ruin the whole structure of the game because you'll create a neverending upward spiral where the DPS and DMG on weapons keep going up and the protections on armor then start going up to compete with the weapon, rinse and repeat.
Here's a simple example: gun A is considered OP, so B and C get buffed to meet A. Once that's done, it's determined that B is now OP, due to some other factor. So, A and C get a buff to meet B. Now, once the dust settles, C becomes OP for one reason or another. One of two things happen with this: 1.) this buff process goes on indefinitely to "balance" everything or 2.) all guns in the same type end up with identical stats and differ only in their model. Both of these options suck.
Now let's take the other side of this. As weapon buffing runs rampant, eventually all weapons start cutting through enemies (NPCs and PCs) like a hot knife through butter. As this weapon buff starts cranking out 250k, 275k, 300k DPS, 500k toughness starts to look more like 200-250k toughness. So, because players will probably be calling bullshit, they buff defense on gear to "counteract" the arms race from the weapon buffs.
This will go on indefinitely until the game becomes beyond broken. So, in order to avoid this, Massive balances the game by adjusting weapons and gear up and down (similar to sliders on an equalizer) to try to keep them destinct but still viable in the game. The unfortunate consequences of this is that the game and gear are in a constant state of flux as they try to even things out.
Now to really complicate things, they have to balance weapons and gear for both PvE and PvP. In a game that's exclusively PvE or PvP, weapons and gear can be balanced and then the enemies can be adjusted to compensate for the changes. However, this isn't easy, as we're all aware based on building your character for one or the other.
Destiny addresses this by normalizing everything in the Crucible, except when you play Irom Banner. That being said, when players play IB they know they can get wrecked if they're undergeared. If you still want to play PvP and not deal with gear bonuses, you can enjoy some vanilla Crucible. Because DZ is basically IB 24/7 with no other PvP option, Massive tries to balance weapons and gear so they're of the same value in both PvE and PvP.
On top of that, there are mistakes where items slip past QA (G36 & AB gloves) for one reason or another and they have to make chances that are bound to piss people off. Unfortunately, some of these just can't be avoided.
IMO, the real problem with weapon and gear balancing in the game is the DZ. If the DZ was either not part of the game or normalized like Destiny, I don't think there would be as many problems balancing. I could be completely wrong, but it's my understanding that Massive's inability to reconcile FrontLine gear and the B.L.I.N.D. rifle with PvE and PvP is why the gear will probably never make it to the game and why the rifle might not be out for an update or two, if ever.
So, that's a lot to digest, feel free to pick it apart.