I am pretty sure freshwater mollies can contract cryptocaryon irritans. However, if they had ichthyophthirius multifiliis prior to coming to a saltwater tank, none of the ichthyophtirius multifiliis will survive. In fact, salt water (at a very low salinity) is one of the recommended treatments for ichthyophthirius multifiliis.
The only time I would quarantine freshwater mollies is if they have been exposed to saltwater before. If they have been in freshwater for longer than a month before the conversion to salt water, I don't think you need to quarantine them.
However, what I said above only applies to ichthyophthirius multifiliis and cryptocaryon irritans. I don't know about other freshwater diseases.