As is often the case in standards bodies when there is disagreement, neither side won, and we left things unspecified. The RFC doesn't constrain how the IV should be chosen, so you can initialize the IV either way.
There was language indicating that the IV should never be the same, as well as an additional method of generating the IV, by using a Linear Feedback Shift Register (LFSR), which also will eliminate the potential problem of related plaintext being sent to the crypto algorithm. So although the RFC doesn't say this, I would recommend either the use of a LFSR, or the last cipherblock in the previous packet encrypted using that key, and to avoid using a simple counter in your IPSEC implementation for the Initialization Vector (IV) in each packet.
So to be fair, in this particular case, the person with "known associations with the NSA" was actually trying to make things better, although he did feel constrained in not explaining all of his reasons in the open wg meeting. Which no doubt tripped Gilmore's paranoia, and I can't blame him for that either.