Its actually quite easy to see why bolt weapons were too good. Compare the weapon stats in Rogue Trader to the ones in Deathwatch (I know because I did this). Not counting bolt weapons, all the others seem to be roughly 2 damage and 2 penetration higher (give or take). You could almost consider this an "Astartes Trait". Now, using that same analysis, look at the bolt weapons and realize that they are just insanely higher, including a full extra die of damage. This alone points out that the stats are in no way balanced.
As far as "nerfing vs buffing". The issue is that bolt weapons were simply over-buffed to being with. You couldn't raise the damage of all the other weapons without REALLY messing up everything. I prefer my fights to last longer than a turn personally.
As H.M.B.C. said, the weapon stats work, and work quite well. I've been using them in my own campaign.

