I would think if both perks just ignored white damage and only took the time and yellow numbers into consideration, that would fix the problem. The white numbers shouldn't have ever been a factor anyway. If you hit a body shot with the black hammer, then the reload should be enough to cancel out the perk. Similarly, if you take too long to get another crit shot with the hand cannon, you don't need the extra bullet.
I think that comment they made about "Why don't you just buff the weak one instead of nerf the others" was very important and insightful, and I wish people took that more into consideration.
Personally, I've barely PvP'd since The Dark Below came out. After the big weapon patch right before tDB the Time to Kill (TTK) feels like it has increased. I find myself regular 3 shot by hand cannons, sometimes 2 shots, I've even been 1 shot by a hand cannon on more than one occasion. Even if we look at the 3 shot kill, though, I find that I have such little reaction time before I'm dead that I can't fight back. This has sucked the fun out of PvP for me. I loved Halo fights where even if someone got the jump on you, if you knew your shit, you could turn around and tie, maybe even win, the fight. Destiny feels more like CoD to me with it's TTK, which I don't like.