I know nothing about motor cars...
Either the fault light is telling about REAL pollution or the electronics that turn it on are imagining pollution that isn't there.
Garages that do MOT tests check car exhaust for pollution - a test there could tell if it's real or imaginary.
The engine management system will (should) correctly regulate the fuel /air mixture for proper combustion. Any pollutants remaining will (should) be dealt with in the exhaust system.
I fail to understand why the garage would want to strip the engine down - I wonder what they expect to find in there?
You might consider asking them - you might consider another garage.
Good luck...
Peccavi
April 2013