There's a notable difference - BUT, it really depends on your use case. General use, non-graphic intensive work, most (again, not graphic intensive) development, office apps, "lite" gaming, even things like 2D graphic apps, you're most likely good.
Two things:
1) The $500 difference is also a 2.5GHz vs. a 2.2 and 512GB flash storage vs. 256, if you upgrade those items on the non-R9 machine, it's only $100 difference
2) There are killer deals in the refurbs on Apple.com, and in the used market, don't be afraid to buy used, I got my machine as a bonus, but I would've gone refurb/used if I was buying. There's a 2.8GHz machine in the For Sale section right now, still has original warranty, like $1800.