So applying Vorpal as RAW the 2d4 and 2d6 gets 2x the bonus in % that a 1D8 or 1d12 would get. But everywhere else the higher the average roll the lower % increase in damage you get from Vorpal.
Your numbers are very close to the one I got, but I think you're missing something. It's not the number of dice, it's the die type. d4s get a bigger proportional benefit whether you're rolling 1, 2, or 10 of them, d12s get a substantially smaller benefit.
There's no way to 'fix' that.
The variation you propose doesn't fix a disparity, it just reverses it. Instead of 2d4 gaining twice the benefit of d8 it gets half the benefit. That's not making it more 'balanced' it's just tilting the 'imbalance' from one to the other. And, your variation is even harsher for a 2d6 weapon. I can't recall the weapon scaling chart off hand, but it would become positively laughable if there are two- or multiple-die larger-die weapons that might exist.
I understand that the mechanic is not perfectly even-handed, and that can seem 'unfair' or 'imbalanced' but it's a simple mechanic that can play out in a fun way for a certain (dice-happy) kind of player. While the damage increase may seem dramatic, for the level of magic item in question, it's really rather meager.
Finally, 2d weapons already behave statistically differently from other weapons. A longsword or greatsword has a linear damage distribution, it's as likely to roll 1 or maximum as to roll either side of average. A falchion, OTOH, is more likely to roll exactly average (5), than to roll maximum, and never rolls a 1. That makes it a more consistent damage-dealer, which is desireable to some, and undesireable to others. On average, it'll deliver more damage when Vorpal, because Vorpal will come up a lot more often, but, when it does, it won't add a whole lot more damage. Vorpal on a long or bastard sword, OTOH, won't come up as often, but when it does it will sometimes do dramatically more damage in a single hit. If you're trying to punch through a monster with high DR against your vorpal weapon, the latter may actually do more damage, and it's also more likely to dramatically finish off or one shot an enemy. If you're grinding through a high-hp/low AC monster, without DR, OTOH, the 2d weapon will whittle it down faster.
In 3e, monster-vs-player balance was such that PCs could expect to win most fights 'on average,' so more consistent weapons, like the 2d6 (19-20x/2) greatsword, were generally better for PCs than swingier ones, like the 1d12 (20/x3) greataxe. In 4e, monsters seem to hit more consistently, and players less so, so I'm not sure if the same will hold true - the advantage that PCs have seems mainly to be healing, and, of course, thier greater variety of powers.
