If you need or want to send a quick letter to an organizational contact, the only way personalize it to them is to include that specific individual relationship type in the export, add in the individual relationship contact name to the merge file and then merge.  But if you have more than one of those contact types, it will merge all of the contacts and then you can print the letter(s) that you want.

If you were able to quick letters directly from the relationship, that would eliminate that step and be able to send to just one person at that organization.