Although this is not a real answer, it's perhaps a good reason to contact your recruiter and find out for sure. When finishing up at high school a good mate went for the RNZAF (back when they flew a bit quicker..). He was ruled colour deficient thanks to those diabolical Ishihara tests. However, prior to this he had gained his class 1 medical after passing the Holmes Wright A lantern test, a similar situation to your own I believe.
Anyway, after chatting to their medical staff via the recruiter they were happy to accept his application as the RNZAF uses the HW-A as their standard of colour testing. He sucked at the interview though so lucked out, but the point is that while the Ishihara is used as a colour screening test, in the case of the RNZAF (and perhaps others?) the HW-A is the definitive test. Being that you are obviously red/green safe, and that is the deficiency they are trying to weed out, I think that you may be alright depending on what the policy is, so definitely contact your recruitment office and find out for sure!