Edward Erin worked at St Mary's Hospital in Paddington, west London.
Miss Prowse became pregnant with his baby after they began a brief affair at an office Christmas party in December 2007.
Last month he was found guilty of two charges of attempting to administer poison to Miss Prowse - once in a cup of coffee and then in a glass of orange juice.
In her first broadcast interview since the trial, Erin's wife told BBC Radio 5 live's Victoria Derbyshire show: "How can the jury not see the science for what it is? How can they basically get it so wrong?"
Dr Edward Erin was found guilty of spiking Miss Prowse's drinks
Dr Erin said her husband "just wouldn't" try to induce an abortion in Miss Prowse.
"What would the worse outcome have been? She would have had this child and he would have had to pay support for this child," Dr Erin said.
"It wasn't ideal but if these things happen, they happen."
She said she was aware of her husband's three affairs but that she did not intend to leave him.
"I know that people have affairs and wreck marriages - it happens. It doesn't necessarily mean that families split up - I want my family to stay together," Dr Erin said.
"We have been together since 1990 and when you are with somebody for that long a time, when you know what they've been through - things in their past, the suffering that they've gone through - you can kind of understand why certain things happen."
I have not married a bad man
Dr Lowri Erin
Dr Erin said her husband had affairs as a "distraction" from problems in his personal life, including a number of deaths in his family.
"He wanted to distance himself from everything and find some release somewhere else," she said. "I have not married a bad man."
Dr Erin said her husband was "very confused and distressed" upon his arrest.
"He said, 'My secretary at work says I have been poisoning her,' and he kept saying, 'Why is she doing this, I don't understand why she is doing this'."
Dr Erin said her husband was "not being treated well" by other prisoners while in custody.
"He is being called a child murderer," she said. "He is a state of complete distress - I don't know how he is going to get through this to be honest."
Last month Erin, originally from Caerphilly, south Wales, was told that a custodial sentence was "virtually inevitable".
Miss Prowse gave birth to a healthy baby in September 2008.
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