I've worked around eC not quite understanding the authorize/capture concept by adding a new workflow status in my payment gateway module. My module also defines rules for moving the orders through the states, however the default "Mark shipped product as completed" rule gets in the way as it marks orders shipped as completed, where I need to capture them first.

Adding a "Transaction allocation status: full" condition to the default rule would solve this problem, and I think it still makes sense outside of my module.