Koontz called the religious exemption "horribly offensive" and hypocritical on Mooney's part.
But Mooney said it's more important to protect the rights of those whose views are different from Koontz's.
"What comes first, religious freedom or the militant homosexual agenda?" Mooney said.
The religious exemption was approved by the committee over the objections of four senators, including Sen. Jennie M. Forehand, D-Montgomery.
"Some of the most prejudiced people I know are the most devout people on Sunday," Forehand said.
When the governor heard about the amendment, he couldn't understand why someone would use their religious beliefs as a reason to discriminate against someone, said Glendening spokesman Ray Feldmann.
The committee also removed bisexuals from the bill on the basis that all homosexuals would be protected from discrimination.
The committee changed the wording so someone cannot be discriminated against "solely" on the basis of sexual orientation.
The committee's gay rights debate was halted when the Senate went into session to discuss a 36-cent-per-pack increase to the cigarette tax.
To continue his assault on the bill, which he claims gives special rights to gay people, Mooney had legislative lawyers draft 15 amendments.
He wasn't sure Thursday which ones he would offer today.
One amendment would prevent gay people from being employed by schools. Another would hold schools liable if a gay person sexually abuses a student.
Mooney would also like to see Frederick and Washington counties exempted from the legislation.
Koontz said Mooney is creating a climate that encourages violence against gays.
"He's now breeding, fanning the flames, of hate and fear," Koontz said.
Mooney said he doesn't condone violence against anyone.
Judicial Proceedings Committee Chairman Walter M. Baker, D-Eastern Shore, said the gay rights bill has divided his 11-member committee.
"I told the governor I'd vote for it. I made a mistake, but I keep my word," Baker said.
The changes by the Senate Judicial Proceedings Committee mean the bill must be returned to the House of Delegates before it can become law. The House has already approved the bill and the changes imperil its passage because time is growing short with the legislature set to adjourn Monday.
The bill aims to prohibit discrimination against homosexuals in employment, housing or public accommodations.