Shouldn't the lens meet Canon's standard of quality no matter where the factory is? Why does it have to matter?
Although, that said, in my business (water pumps) we (in Australia) recently had a job come from Thailand, we had to design it here (where the design knowledge is), but we had to get the pumps made in the facilities in Singapore, so they would have the "Made in Singapore" nameplate.
Why? Because the Thai government has some policy that they can only buy from local-area manufacturers (we don't have a plant in Thailand, so the closest was Singapore). Makes no difference to the final product, if we'd built it here in aus it would have been the exact same parts (we buy our pump-parts from Singapore anyway), just "assembled in Australia".
(and at the end of the day, all of the profits made go back to Head Office in Europe anyway...)
So sometimes country of origin does matter (even if there's a fair chance that the raw ingredients are imported, there's a fair chance that anything made in Asia these days is using Australian iron ore). That's mostly for governmental policies though, there shouldn't be a quality difference.
Actually, in this case, i'm glad these lenses are made in Malaysia. Note how they're available aready? Note how all the über whites were delayed for over a year? That's the real difference between 'made in malaysia' and 'made in japan'...