I really don't get it, tbh.
They had two projects in development, one of which was retooled from a project BHG already had when in development. All the initial design stuff was covered for both projects due to Copernicus' development, from the history to the art style. That should have shaved a decent amount off the cost of the projects. The MMO was set to launch next year, and it
looks good. The fact that EA was publishing only reduces their cost (though also reducing their profit--though they clearly judged it to be advantageous).
It might be that they weren't actually receiving royalties for the game, since EA was publisher, but actually had to sell 3 Million copies to get their full payment. PC games are also vastly more profitable for the company, because they don't need to pay royalties to the console maker. Problem is that those royalties are paid upon printing, not sale--every physical console copy means money paid to Sony and Microsoft, so unsold copies are an even worse loss.
What boggles my mind is the timing. Last year's final quarter was absurdly loaded with big name titles. I worry that they launched KoA at a poor time simply because they couldn't afford to really wait. Which honestly sucks, because if they had launched it in late April/early May, I think it would have done really well.