I can't imagine Nifong taking out the semen sample from the rape kid before sending it along for analysis; he hoped it would contain the DNA of the players.
But it's almost unimaginable that the first DNA tests came back negative for semen. If defense attorneys got the first analysis back from Nifong's office instead of from the lab, however, he could have removed the section which talked about semen presence which DIDN'T match the players is the scenario I'm picturing.
I find it unimaginable that there was semen from only one person and no evidence of condom use. She was an escort. I wonder what her specialty was then.
Your theory is very plausible and likely correct. My theory of a crazed Nifong feverishly throwing things in and out of the kit like Dr. Frankenstein, aided by his faithful hump-backed Igors Gottlieb and Himan, is more satisfying to me though. Like Frankenstein, he has personally created a "monster" out of flawed parts.