The Christian owner of a bed and breakfast has been ordered to pay damages after a court found her refusal to let a gay couple stay in one of her double rooms amounted to direct discrimination and a breach of equality law.

Michael Black and John Morgan brought a civil case against Susanne Wilkinson, who owns the Swiss Bed and Breakfast in Cookham, Berkshire, after they were refused accommodation at the premises in March 2010 despite having made a reservation and paid a deposit.

In a verdict delivered on Thursday by recorder Claire Moulder at Reading county court, Wilkinson was ordered to pay £3,600 in damages to the couple, who said they were shocked and embarrassed and felt "like lepers" after being told they were not welcome at the B&B because their same-sex relationship was against the owner's convictions.

The verdict found that Black and Morgan, from Brampton, Cambridgeshire, suffered direct discrimination by being turned away from the guesthouse because they were gay. Moulder said that by refusing the couple access, Wilkinson had "treated them less favourably than she would treat unmarried heterosexual couples in the same circumstances".

In a statement, Wilkinson – whose legal defence was paid for by the Christian Institute, a national charity – said she was giving "serious consideration" to an appeal against the ruling.

"Naturally, my husband and I are disappointed to have lost the case and to have been ordered to pay £3,600 in damages for injury to feelings. We have the option to appeal, and we will give that serious consideration. We believe a person should be free to act upon their sincere beliefs about marriage under their own roof without living in fear of the law. Equality laws have gone too far when they start to intrude into a family home."

But the decision prompted relief among equality campaigners. James Welch, the legal director of Liberty, said: "Liberty defends the rights of religious groups to manifest their beliefs, even when we disagree with them. But it is simply unacceptable for people running a business to refuse to provide a service because of someone's sexual orientation. Hopefully today's ruling signals the death knell of such 'no gays' policies – policies that would never be tolerated if they referred to a person's race, gender or religion."

Lawyers for Wilkinson had argued that she was entitled to refuse double rooms not only to gay couples but also to couples who were not married or in a civil partnership. Black and Morgan are not in a civil partnership.

But the judge found that although the refusal of a room could be seen as a manifestation of the owner's religious beliefs, her right to manifest those beliefs was not unfairly limited by the Equality Act of 2010, which requires that service providers do not discriminate on grounds of sexual orientation.

Wilkinson and her husband say they have received two years of abuse for the decision, which enraged gay rights campaigners but gave succour to some Christians' claims of persecution.

In her statement, Susanne Wilkinson said: "People's beliefs about marriage are coming under increasing attack, and I am concerned about people's freedom to speak and act upon these beliefs. I am a Christian, not just on a Sunday in church, but in every area of my life – as Jesus expects from his followers.

"That's all I was trying to do and I think it's quite wrong to punish me for that, especially after enduring over two years of vile abuse and threats. We find this a strange justice in a society that aspires to be increasingly tolerant."