This is going to be a fun story to read. I could see where this would be like Reptilia's "Light's Hope, Death Hunters", Where Harry and Hermione become mercenaries.
As for ships, of course this would be a H/Hr, but maybe add a couple others. They could form a task force. I have always liked Daphne Greengrass and Susan Bones. I could see where both of those would add much to any force. They know both sides of the Pureblood politics (light and dark) and who's who in society.
You could also add Neville with Hannah.
Looking forward to reading more.