Feeney, who has young children, said Monday that her behavior "was a huge mistake and unlawful," and that she was sorry.
The boy's mother read a statement to the court in which her son thanked whomever it was who reported Feeney's behavior.
"I want everyone to know, if it wasn't for this person, there was no stopping Mrs. Feeney," the boy said in the statement.
Feeney's attorney, Thomas A. Bergstrom of Buchanan Ingersoll & Rooney in Philadelphia, said what occurred was inappropriate and unlawful but called for balance. "This case involved a single kiss," he said.
Judge Thomas G. Gavin pushed back.
"The greatest nightmare all of us as parents have today is, we put our kids in places where trust should not be an issue," he said. "There is no such thing as an innocent kiss."
The boy's father said Feeney's behavior had caused lasting damage to his son and family members, and Feeney was ordered to pay the cost of his counseling.
"Our son was a happy boy before he met Emily Feeney," he told the judge. Now, he said, his son goes to therapy for post-traumatic stress disorder, anxiety and depression. His grades have slipped and he has no desire to go to school, his father said.
Feeney, who was fired last year, was arrested in August. She has been out on bail.
She and the student sent more than 9,000 text messages and emails to each other.
In one message to Feeney, the boy wrote, "I'm not interested in you end of story I'm 16 I'm not into you," according to police documents.
Feeney begged him to talk to her and threatened to call him to her office, according to a criminal complaint. In one email, she said, "You are gorgeous and this is killing me. Please talk to me."
After Feeney recommended the boy for the Harvard swim team, she allegedly wrote to the student, "You...owe me big time. And no high fives."