Is completely wrongheaded.
The problem is that the Tories aren't targeting churches, etc., with their bill (well, they are a bit). They make a big stink about churches and stuff, but the Supreme Court and the law itself are crystal clear on that issue. The Catholic church is not going to face a (viable) Challenge that it won't marry Adam and Steve.
Their bigger concern is justices of the peace or civil marriage commissioners. Quite a few provinces (I think Sask. and Man.) have told their civil officials that they will be fired if they refuse to perform the marriage. Ontario, I believe, did a compromise, that an official can refuse provided that the official finds a replacement.
The provinces that require it have it right, and that's what stresses the Tories.
The problem is, of course, that people acting on the behest of the state are acting for the state and only the state. Performing a civil marriage is ministerial: provided that the couple are qualified (adult, not related, filled out the paperwork), they qualify to be married. Period. There is simply no discretion on the state's part. The person performing the act is acting as the state and that person's personal beliefs have nothing to do with it.
What happens if we go down this slope? Then, any person who is charged on acting on the part of the state can get around all the equality guarantees of the Charter, can get around the separation of religion and state, simply by saying it is against their religious beliefs to do anything. Theoretically, police officers are meant to apply the law universally. What if a Christian or Jewish police officer sees a Canadian law that prohibits something that (in their belief) their religion allows? Do they turn a blind eye? Every single governmental department then becomes a minefield: You get one official whose beliefs allow for one thing, and another whose beliefs allow for another.
I don't see how this can stand up in Court. Think of the downsides. Sure, in Toronto, there is probably someone who can stand in for the official. But what about in a small town, where there is likely only one person who is permitted by the state to perform a civil marriage? Is a same-sex couple there without recourse, if the official refuses?
And what would we say if you substituted "same-sex" for "inter-racial" or "different faith"? Are we going to protect the rights of civil marriage commissioners to refuse to marry divorced Catholics? Or blacks and whites? Or Jews and Muslims?
The civil marriage act is about civil marriage, and the religious views of ANY of the parties--the officiant and the couple--is completely irrelevant.