Indifferent. In AF it will prevent movement of the focus ring but if the ring is forced somehow, it could cause damage to the focus gears or motor (if it isn't full time MF capable). In MF, you don't have to worry about damage to the gears, but the lens itself may now loosen up and may cause added wear and tear on the lens from actuating.
Both cases are unlikely to be a problem though. Personally I leave my lenses on AF mode simply because I prefer to have them locked down when in storage (or they are full time MF and it doesn't matter either way).