Every option people who advocate for ROG/NIN to be usable as a new class has been set out purposely to not be lore breaking. Actively proving this can be done without breaking the lore, helped a lot by the class itself being based on shadow and stealth work and always being a secret.

Remember the Rogue guild is set up, Thancred is a rogue you will learn that from the same guild that taught him, guess what this guild was around before the main story and was most probably active during the main story, this isn't changing any lore it's truth.

Finally if you care so much about it breaking the story, guess what it does jack shit to your story, yours has already been told. all it takes is a bit of fleshing out the Rogue and Ninja story and boom it fits perfectly for new characters who are the ones who will experience this new view on the events, your character won't cause that part of the story has already been told to you.

blocking content of this kind behind the majority of the story only matters to new players, and it's in the players and devs best interest that this content be open from the get go.