From a lore standpoint it is very true that making it a starting class would be detrimental to the story. In fact I could see the Rogue guild being completely empty until you progress further enough into the story, or else you'd have the same issue.

From the MMO standpoint, it makes sense to open this class from the get go, as some people may join the game because they heard ninja was coming, or like to keep to one class and want that to be NIN.

There is the option of your opening cutscene when you start the game as rogue involving you coming from doma then using some form of time travel so you relive the events, with the ninja story tying into why you'd need to travel back to that specific time.

Honestly I don't think the creators would want to add something that went against the story they are trying to tell, so I think you will have to progress far enough through the main quest to unlock Rogue but in the end it could go either way and it's up to the devs.