Well, I avoid "may their memory be a blessing" to friends whom I know are atheists, because the notion of "blessing" can be seen as explicitly theological. I'll sometimes rephrase it as something like "May their memory be an inspiration" or "a source of joy" instead. Naturally, some atheists do use the word "blessing" to mean things like "a source of joy" or "an inspiration", but I find it's probably safer to avoid the word unless I know they use it themselves.

On the other hand, if I know someone is religious, in ANY religion which has the notion of "blessing," I do use it, because, like you suggest, it can be broadly applicable without being too pushy of any specific set of beliefs.