Children can and do break with their parents religion as they grow up (and do so /often/), so clearly it's a choice. Sometimes it's a hard choice. But it's still a choice that's frequently made.

But if you've got amputated legs, you can't choose to just hop up out of your wheelchair and go for a run like pretty much anyone else can.

Perhaps I can make it a bit more black and white. A few suburbs away from me there was a Turkish man who killed his daughter for 'dishonouring' his family (had premarital sex). Now, I am in Australia, and this kind of thing is seen by us as murder, but it's seen by folks where this man came from as honourable.

Should we be saying "It's just cultural, he didn't have a choice" or should we be saying "we're striving to create an egalitarian society, where everyone is treated as equals"?

This man had a choice and to argue that "it's just cultural" (of which "it's just religious" is a subset) deprives others of their freedom to be. Laws need to cover people equally or as said elsewhere you simply create another form of discrimination. This doesn't mean that laws don't need to change, but instead that they should be worded to allow everyone the same flexibility, not having to pass some sort of highly subjecting 'faithness' test.

For the record, the Turkish government has started handing out harsh punishment in an attempt to knock out "honour" killings.