Since you paid with a credit card, I would go that route. It is simple and will save you from wasting time and energy on fighting it.
First, tell them you believe the contract is invalid due to the change order required to meet fire code.
Second, ask for your deposit back.
If you don’t get it in a reasonable time, file a claim with the credit card. Send them the contract and all the details. Those cc companies are really good about fighting for you.
Recently, Chase Visa got a full $1100 deposit out of an unscrupulous VRBO host. He was a complete dick until I filed the visa claim. He kept calling me, leaving voice mails asking me to negotiate and “work something out.” I just ignored him and Visa got it all back. Asshole. But I digress.
I’d go to dixieline and order windows, then find a good independent installer to put them in. These big “reputable” firms are really just expert marketers. They aren’t any better than a good handyman, really, when it comes to doing the work.
Even if you forfeit the $1000, you will come out ahead that route. I may know a couple installers if you have trouble finding them but everyone is sooooo busy right now.