In a statement issued after the hearing, Reyes said, "There's a strong possibility I could end up in jail. It's really sad it's come to this."
Reyes' decision to baptize his daughter without his wife's permission resulted in what some are calling an extraordinary court order: Jordan in the Circuit Court of Cook County, Ill., imposed a 30-day restraining order forbidding Joseph Reyes from, according to the document, "exposing his daughter to any other religion than the Jewish religion.
The couple married in 2004. Joseph Reyes was Catholic, but he says he converted to Judaism to please his in-laws. He has said the decision wasn't "voluntary."
Despite his conversion, Reyes, 35, said he never stopped practicing Catholicism.
When the marriage fell apart, Rebecca Reyes, 34, got custody of their daughter. Ela has been raised Jewish and attended a Jewish preschool until her father decided to baptize his daughter without consulting his wife.
Joseph Reyes sent his wife pictures and an e-mail documenting the occasion. Rebecca Reyes responded by filing for the temporary restraining order, which the judge granted.
Stephen Lake, Rebecca Reyes' attorney, said his client was shocked at her estranged husband's actions.
"Number one, it wasn't just a religious thing per se, it was the idea that he would suddenly, out of nowhere without any discussion and have the girl baptized," Lake said. "She looked at it as basically an assault on her little girl."
Furthermore, Joseph Reyes had never been a particularly devout Christian, Lake added.
When the girl's father took her to church again in violation of the order, he called the media to witness the event.
A court could rule today on whether Reyes should be jailed for criminal contempt, but he contends he did nothing wrong.
"Going to church, I don't think I violated the order," he told "Good Morning America." "In terms of Judaism, based on the information I was given, Catholicism falls right under the umbrella of Judaism."
Click HERE to read and comment on the full transcript of Chris Cuomo's interview with Joseph Reyes.
In a YouTube video of the subsequent visit to church, Joseph Reyes says, "I am taking her to hear the teachings of perhaps the most prominent Jewish rabbi in the history of this great planet of ours."
Lake, Rebecca Reyes' attorney, said Joseph Reyes had never been a particularly devout Christian.
"This was just something that he knew was going to have a negative effect on [Rebecca Reyes], and I think that's why he did it," Lake said, speaking of Reyes' church visits with the little girl.
"I think he was just trying to exert some power," Lake said.
But Reyes, who is studying law, said he only wants to be a good father to his daughter and expose her to his faith. That's something the courts usually allow in divorce cases, experts say.
Eugene Volokh, a professor at the UCLA School of Law, said a parent who has visitation rights "usually has the right to expose the child to his religious beliefs, teach the child his religion, to take the child to religious services, unless there seems to be likely psychological or physical harm stemming from that exposure."
Family court law expert Lynne Gold-Bikin said Reyes should have followed the court order, and said, "If this couple made an agreement about what religion to raise their child, then it's an appropriate order."