Shortening the longer leg is much less invasive and probably preferred, but the discrepancy has to be caught very early. You need years of measurements to predict exactly how long each leg will be and when. If you have those, there’s a pretty small window when the long leg is exactly the right length to tell it to stop growing.
At least in my dialect (US northeast) clothes and close don’t quite share a pronunciation. They’re similar enough that you could probably fully elide the th sound, and I’m not sure anyone would notice.
When I pronounce clothes I can still feel my tongue move into the th position, and hear a small difference.