Well the D was the first operational and it did not have that failure rate that the A,B, and C, models had. I doubt NASA would have ever launched a version that didn't have a high nineties success rate.
That's flat out not true. Take a look at the list of Atlas D launched and look at the failures. The first time they strapped a Mercury capsule to an Atlas D is failed. There was an Atlas D failure in February 1962, and Scott Carpenter rode it for the first manned flight only 3 months later in May 1962.
The day before Walter Schirra launched there was an Atlas D failure.
Two months before Gordon Cooper launched there was an Atlas D failure.
What I don't know is how much they were pushing the limits on the other tests vs the manned flights, or how much more QA they were putting into the manned rockets, but it is certainly not the case that NASA only flew on rockets with high success rates at that time.
