The statement itself, "have a blessed day", isn't necessarily a religious statement. If I where her, I'd discuss it with my boss from that angle. As defined by Websters, "blessed" can have a religious connotation, but it's also defined as: bringing pleasure, contentment, or good fortune. Why then would telling someone to "have a blessed day" offend them. I'd appeal to the managers sense of logic. If that fails, she has to be willing to lose her job over it. In the context of the current economy (and this is just my opinion here) you, and her would be better served by her changing the statement. She may have to lead by example in this situation. Her taking a stand, may be as simple as being the better person. I'm obviously not God, but I think he would understand.
PS: anyone reading this, please don't argue with me about God being a "he". That's not my point!