Quakers must marry only other Quakers, and do it in a Quaker service....so, as they married in a civil ceremony, and she was a member of another faith, Nathan would surely have been disowned by his meeting.....there should be a record of his dis for marrying out, in his meeting, if he was a practicing Quaker at the time. Howeer, this record would have no mention of the bride's name...only the dis'ed member, so no Quaker records will be of any help with the bride or her family. If you're still wanting to search Quaker records for Nathan and his parents, Earlham College, in Richmone Indiana has a lot of mid-western meeting records...you might want to see what they can offer.
Do you know when Susan Ann died? and where? A newspaper obit should contain info about her parents, as would a death certificate. You might want to check the historical society in the county where she died, to see what they have...many have newspapers on film that are available through inter-library loan.