I actually have a stupid fanwank for that, but it's, well, stupid.
So, Bruce Wayne made her new civilian ID. Taking a page from Superman's civilian ID, he makes it someone who has access to information about threats. Since it's Wonder Woman, he makes it someone with access to global scale threats. He makes her an intelligence analyst. However, this is Diana we're talking about, and even when she loses her powers half the time, she's still Diana. She wouldn't be sitting in an office waiting around while others do the day-saving. She applies for field duty, and because she'd effing WONDER WOMAN--even if only half the time--she makes it into the field. So Wonder Woman's own temperament causes her to become a secret agent.
Doesn't explain why Bruce wouldn't have thought of that. Maybe he was still stuck in his "Secret IDs are different from costumed IDs" mentality.