Alas, there are some mechanics working for Toyota who only know the newer cars.
Seriously, they suggested the ECU could require replacement? What a load of bollocks.
Just get your clutch replaced and if your not sure how to reset the ECU, a battery disconnect and reconnect should do the trick.
As another user suggested, a gearbox oil flush is a good idea(I take it you have your gearbox oil replenished at the required intervals) and definately make sure you are talking with a mechanic with some experience on the MR2 models, I've had issues with mechanics who didn't know the vehicle and simply getting someone who understands MR2's relieves a whole lot of stress as other users have also mentioned.
Sometimes it can also help to purchase your own clutch kit as often Toyota or any mechanic and auto-shop will not have the spare part in stock. Exedy to a nice kit but there's also even cheaper alternatives if you want to save some cash. Repco can obtain cheaper kits. Oh and on the clutch kit purchase, don't be fooled by race style kits, you will find them to be harder and hence require a touch more pressure to engage the clutch, so if your used to the stock clutch, then Exedy or if you can still get the original(myself I have an MK1 so I didn't have a choice but to source an aftermarket) is your best bet.
Please let us all know how it goes and I hope your driving off into the sunset in that glorious MR2 pumping your favorite tunes from your stereo soon.