I'm a mechanic. There's zero chance they fucked up your car on purpose just to make more money off you. That's a big misconception about this line of work... we really have no incentive to do that and big chain stores like pepboys have strict policies about work being done and documentation. No mechanic is going to risk his job for $30 which is what he'd make replacing your spark plugs.

Having said all that. It does sound like there may be some misdiagnosis going on. When there's a misfire, it's very common for people to assume spark plugs without doing any testing. What the car really needs is a diagnostic service to figure out what the problem is. Knowing nothing about your vehicle I can say usually a random occasional misfire is going to be caused by a bad coil or if it's an older vehicle, cap + rotor + wireset or something. It could just as easily be carbon buildup in the throttle body, clogged fuel injectors / fuel filter, fuel pump not building pressure, etc.

Based on your description it sounds like it really is just a coincidence. You said it ran fine for 2 weeks after the service, and there's really nothing in a thermostat job that could cause those symptoms. I'm assuming they didn't replace the spark plugs and only reset the code light for you. If they DID replace plugs then my best guess would be that they used non-oem plugs. But again you'd more expect to find an occasional random misfire if that was the case, not a dead cylinder with no power. You really need a compression test and a proper diagnosis.

By the way all this is expected with higher mileage vehicles. I don't know how many you've got on your odometer but the only way to avoid this kind of maintenance is to just buy a new car. For most people it's cheaper to spend $1500 a year on maintenance than it is to buy new though. I know I'm definitely one of them lol.