I think it should be allowed, here's why:
1) You are in no way altering the game, or cheating in anyway. You are just taking advantage of a glitch. The principle is no different than the statue or train strat.
2) The controllers you are using, are standard N64 controllers, and thus both are 100% legal according to the-elite's policy.
3) If "was this run legitimately done by one person?" ever is asked, think about this:
Anyone of us, and I mean anyone, could be two people. One person could be using the control stick + Z, and the other, A, B and Cs. This should not be a question ever now, since it was never before, and the circumstances aren't really all that different in my personal opinion.
4) Anyone who can actually learn and play with 2.3 deserves a WR or commendable disctinction, since it must be so damn hard.