I’m so sorry to hear this, Bubbles! You’re right that he’s safer inside. If it helps, you could show your family this page on the dangers of making a bunny live outside in a hutch: https://rabbit.org/faq-rabbits-outdoors/
How old is your bunny? If he’s not old enough to get neutered yet, he should soon. You can find details on litter training here, though it sounds like you’ve already read up: https://rabbit.org/faq-litter-training-2/ In my experience, it’s hard to keep *all* poops in the litterbox, as some stray ones do tend to find their way around the places bunnies are allowed to go, but you should definitely be able to make sure all the urine stays in the litterbox.
I work all day from home in the same room where my bunny lives, and the smell is not bad unless I’ve just changed the litterboxes. I use CareFresh litter and an AirSponge odor absorber near where I sit.
If your bunny is still not old enough to be neutered and effectively litter trained, could you compromise by keeping him out of certain rooms, or keeping him in an exercise pen most of the day?
Good luck, and good for you for looking out for your bunny!