If it's a chain I would consider taking it over to the main location to make your case. It's terrible to see what some installers will try to get away with when they don't have any meaningful oversight.
Small independent shops/shop owners are usually the best to deal with. They generally won't risk their rep with any of the hack-n-tac clownery, where the chains will often hire anyone standing with a pulse.
If you were my brother on the other side of the county, and they don't offer to make you whole, I would say to you document everything, get two estimates for all damages including OEM for the glass ( not a chance it left Toyota that way with a scraping gouge in it ), film removal, detail and two days of car rental. Add to that any ammount paid up front and write a letter of demand served through a process server to their registered agent (available by looking up their article of incorporation/ secretary of state)
They will look stupid in small claims if they refuse and likely have to cough up for it. Maybe have an attorney write it if you have someone local for contract type writing and add the cost to your demand.
This may sound like overkill until you find out how much the factory glass replacement is. I would force them to make you whole. You sound like a mild guy and may not want to go this route. I personally would hold their nose to the mat and make them tap out, either up front like an honest biz, or in small claims. That's the cost of poor employee screening. eff 'em.
When you get ready for your next car, you can always post a request here on Tint Dude and someone will most likely have a good referral for you in your area.
Replacement is up to you, how bad that scratch bugs you. It can be touched up with paint to hide it a bit.
Personally I wouldn't trust them to remove the film, they'd probably just leave all the clear adhesive behind for the next guy to deal with. Tough call because now you have to pay someone to remove and replace it.