Don't you have to go with the shorter recension with today's critical methodologies? You really have no other choice. And the fact that the shorter recension explicitly supports transubstantiation and the longer has nada on it means the longer has got to go. :)
If the longer recension was proved tomorrow to be the genuine one, it wouldn't bother me a bit. There are other writings from the 2nd century besides Ignatius which affirm that the Church held to a decidedly non-Zwinglian view of the Eucharist.
That being said, it's an extra bonus that the short recension is the genuine one. :>)
Pray for JP II