Judge Andrew Rutherford's ruling against the Cornish Christian couple who refused to offer a double bed to a gay couple treads a narrow line in deciding what counts as discrimination. It will no doubt delight the evangelical Christians who can use it to strengthen their own sense of being a persecuted minority, but the real point is a more subtle one, about the equivalence of civil partnerships with marriage. That may well increase the rage of conservative evangelicals, but it is unlikely to win them many converts.

A spokesman for the Evangelical Alliance seemed for once to blame the law rather than the judge for his ruling: "Human rights law needs to face up to its current lack of fairness and inability to decide even-handedly where rights clash. This applies particularly to religious conscience and practice in public life."

The important point about Peter and Hazelmary Bull, the couple who owned the Cornish hotel in question, was that they really believed that their policy did not discriminate on grounds of sexual orientation. Their line was that no unmarried couples, whether straight or gay, could share a double-bedded room, and evidence was presented to show that they had previously been in trouble with heterosexual couples who had been turned away for this reason, as far back as 1996.

They did not, by the way, object to letting such immoral couples use twin-bedded rooms; as Judge Rutherford observed: "Two persons of the same sex … who have come to Cornwall intent on a sexually fulfilling weekend may enjoy that weekend to the full in a twin-bedded room. Putting it bluntly, the hotel policy allows them to do so albeit in the confines of a smaller bed."

So it really does appear that the Bulls were attempting to run a policy that did not discriminate against gay unmarried couples any more than it did against straight ones. The judge is quite clear that this is a clash of genuine rights and sincere principles on both sides. His job is to balance them, or rather to discover how the law balances the two rights – to the free exercise of religious belief; and to freedom from discrimination on the grounds of sexual orientation.

The crucial factor turned out to be the fact that the gay couple, Martin Hall and Steven Preddy, had entered into a civil partnership. The law says that civil partners are to be treated as married ones and in that sense the Bulls' policy was direct discrimination, since there was no possibility of marriage, still less Christian marriage for any gay couple. That is why they won their case.

Had they not been in a civil partnership, things might have been very different. That's clear from Judge Rutherford's statement: "I say nothing about what would have been the position if the claimants had not entered into such a legal relationship or indeed if they were a heterosexual couple." So there is still an opportunity for another lawsuit.

But the real difficulty for evangelicals and Christian conservatives does not come in the actual terms of the judgment, but in the background from which it is drawn. In particular, it is the preliminary remarks of the judge that will cause them pain: "Whatever may have been the position in past centuries it is no longer the case that our laws must, or should automatically reflect the Judaeo-Christian position." He goes on to quote Lord Justice Laws, in his ruling over the similar case of a Relate counsellor dismissed for refusing to offer sex advice to gay couples: "The general law may of course protect a particular social or moral position which is espoused by Christianity, not because of its religious imprimatur, but on the footing that in reason its merits commend themselves."

The real pain caused to conservatives is that these are not the rantings of dogmatic secularists, but of pillars of the established church. Lord Justice Laws is reported to be a devout Anglican; Judge Rutherford was until six months ago the chairman of the body that negotiates the rates paid to ecclesiastical lawyers. If nothing else, this suggests that the laity of the Church of England no longer believe in establishment.