Advice a newb: Brake Actuator

So, I've always lurked the forum when anything arises with my 2006 Prius. I always find advice and solutions to my problems, but this time I need something a little more... responsive.

I have a 2006 Prius, the ABS light came on along with the now permanent red Brake light. After a couple days of researching and tinkering I took it in to Toyota and after a day the call me and tell me it's the Break Actuator, and it will run me around $1,800.00 for repair. I asked if there was anything else I could repair to bypass the Actuator or anything that would make it drivable for at east another couple months. Or even something to cut down the cost. He said there wasn't anything aside from possibly financing the repair costs. I said I was going to sleep on it. Then I come on to the forum do some reading and find out about the warranty on the break actuators extending as far back as covering the 2006 models still. I call the next day and with a very firm attitude I say that I've checked my warranty information and the actuator is definitely covered 100% by Toyota. He puts me on hold and comes back, "yes, you are right. I'm sorry we missed that." Even though I was happy with the warranty covering my repair, I was flabbergasted that they wouldn't know or even try to find out if it was under warranty. Followed by a simple, "my bad" that could've cost me 2k.
Anyway, fast forward to 5 days later when I'm about to go pick up my car they he tells me another light came on after we put the car back together and that the car won't start but they're sure it's something unrelated. They need time to check. They finally call me back and say it's the transmission and will do me 5 grand in repair and labor. And that the car is not drivable any more.

Now, having been on the repair business, I understand things like this happen. But I am extremely irritated by their approach and how certain they are, even before they identified the second problem, that the new issue was completely unrelated.

Does the possibility exist that they could have messed up the transmission while working on the brake actuator? I do realize my Prius has 180k miles, but I have always taken it for yearly maintenance and never has any problem with the engine or transmission shown its face. What should I do? Should I just part ways with my Prius and not worry about it? All I took it in for was because the lights remain lit on my dashboard and now they say the car is undrivable.