Well, apparently this is all just a big misunderstanding of some sort, but I agree that you should know as much about the organizations to which you donate as you can.
My charitable donations go to secular organizations; I'd prefer to avoid an agency acting on its own agenda and imposing its own morality, rather than just providing donations to needy recipients.
CBC also ran a story on this issue; it appears to be a policy of the Calgary branch of Sally Ann, not a national policy: http://www.cbc.ca/canada/calgary/story/2010/12/09/calgary-salvation-army-harry-potter-toys.html
So yeah, it is still a policy, just not at a national or international level. So the point remains that yes, you should know as much about an organisation you donate too as possible. I mean, if you're just handing in a few toys, it's understandable to not know all that much, but for bigger donations at least, reading through some information first would be advisable.
I don't think that completely missing religious based organisations is necessary. You just need to be careful which ones you donate to. But church based organisations largely do not have disagreeable agendas (i.e. charitable agendas tainted by theology).