The 2fer deal is Q fares which is different than what you normally get @ the cheaper rate from their website. They are still economy however. If you care about miles, the free ticket does not accumulate miles.
There's more flexibility with the 2fer deal in case you need to change your flight schedule. I believe the rep should have already told you the advantages when you got your quote.
Have you looked at other airlines too? I got quote for 1.8k for this May, and I was able to find cheaper deal elsewhere. It really depends when you are going. Sometimes the 2fer deal is better than anything else.