I wouldn't allow it, because with Greater Magic weapon, all you need is +1 on your weapons anyway. To remove that +1 would lower the cost of special abilities for weapons below what they were designed to be.
For example, you could get a Vorpal Keen sword for 72,000gp instead of the 98,000gp it was designed to cost. With Greater MAgic weapon, the fact that it has no inherent plus is hardly a downside.