Note there is a difference between SmcFanControl and HDDFanControl.
SmcFanControl sets the lower limit of any of the system fans. This can help keep your iMac cooler at the expense of noise, but will not help correct the problem you are having which is a disconnected HD thermal sensor telling the iMac's thermal control firmware that the hard drive is very hot, so it spins up the hard drive fan.
For what you have there are two solutions:
- Replace the thermal sensor using the hardware solution linked above. This is the best solution as it doesn't require any 3rd party software and keeps the iMac's functionality as close to the factory original as possible.
- Use HDDFanControl which will override the control of the HardDisk fan by overriding the SMC Thermal control software and controlling the Hard drive fan using the thermal sensor retrieved from the drives smart status.
I actually use both SmcFanControl and HDDFanControl on my iMac with two internal SSDs. I found that just using HDDFanControl can actually make the other fans default settings not work correctly. If one fan pushes too much air out the exhaust it will cause the other fans to not be able to push air through when they are at low speeds because they all share the same exhaust. All 3 system fans need to be balanced..
You can get HDDFanControl here:
http://www.hddfancontrol.com/gettingstarted/installing-hdd-fan-control/
I haven't tested it on Sierra yet.
If it were me I'd go back to the repair shop, tell them if they are working on iMacs they should know that they need to add a thermal sensor like the one above. Tell them that you will pay the cost of the part, but they should make it right and cover the labor to open up the iMac and put in the cable. If they refuse to, leave them a bad review, and find a different repair shop that knows how to work on iMacs and take it to them.
If they want to rely on a software solution for this they should 1) Make it clear up front 2) recommend a software solution that actually solves the problem and 3) install/provide the software and set it up as part of the service.
I don't have the hardware solution because it wasn't available when I first replaced my Apple drive but the software was, but I would prefer the hardware solution. I don't want to open up my iMac again, but if I ever have too I may switch over.
There are probably other Fan Control software applications that will do what HDDFanControl does but I haven't investigated them. The SSD Fan control application you are using may be functionally equivalent.