I've seen people set up a '2nd Email Address' field and have a secondary address sat in this field so you can see there are two addresses, but you wouldn't be able to email both email addresses (that sounds like you don't want to do that anyways).
You could then merge both the records and still have a record of both email addresses.
This is definitely a unique situation and I am sure a lot of people handle it differently depending on their business. I agree with Juli about using a secondary email address field.
Check out this thread, Gregoire gives some helpful tips on creating 2 additional email fields and using a smart campaign.