Well, I have a 15-inch MacBook Pro and I hardly hear the fan. So, I don't know about it.
But, looking at both the laptops, I would recommend one of the following configurations:
13-inch rMBP: 2.6 GHz Core i5, 8 GB RAM, 256 GB SSD: US$ 1,499.00
13-inch MBA: 1.4 GHz Core i5, 8 GB RAM, 256 GB SSD: US$ 1,299.00
A US$ 200 price difference for a retina display and a faster processor. The downside is that the Air is a little bit lighter and has more battery life. Overall, I would go for the Pro as I think it is more worth it.