At the age of 36, Bowyer is among of the world's oldest living survivors of the disease. There are three over the age of 40, and only one over the age of 50, said Justice Patricia Courtney.
He has to receive specialist infusions once every three weeks for his disorder and faces a high risk of death if he gets an infection.
Justice Courtney said Bowyer was likely to be dead within a decade and the illness had likely affected his judgement, contributing to his involvement in the drug smuggling operation.
During his time as a supplier of MDMA, Bowyer was a high-powered Microsoft employee earning $205,000 each year before benefits.
Justice Courtney ruled a jail term would likely bring a risk of a deadly infection and prison staff were unlikely to respond with emergency medical attention as quickly as needed.
She also ruled that Bowyer's role in the syndicate was a minor one, and wasn't undertaken for financial gain.
"Your involvement in drugs was out of character and a massive error in judgement on your part," she said.
"Good luck for the remains of your life. I think that you should be humbled and grateful for the level of support that you have had."
The public gallery of the court was packed with Bowyer's teary parents, sister and friends.
Two friends, who wish to remain anonymous, said outside the court how relieved they were at the sentence considering his health conditions.
