I've had to return a system to an Apple store once. Until somebody comes along that has done it through mail, I will offer a quick recount of my experience, which should give you at least some idea of what to expect.
It depends on whose hands the system ends up in when it's received. But, usually, it will be inspected for physical damage, and is then supposed to be powered on to verify that it still works and that none of its hardware has been replaced or removed. This can happen the same day in which it's received, but it depends on how busy they are at the time of receipt. So, I would give them 3-5 business days, and then start calling if you don't have a refund by then.
The Genius that took receipt of the one that I returned merely did a quick visual inspection for damage, and then gave me in-store credit which I immediately used to get a beefier system. FWIW, in my case, the dual-core CPU of the 13" i7 did not meet the needs of the virtual machine workload that I was putting on the system. So, I upgraded to a quad-core i7 in the 15", and never looked back.
Did you actually ask for a refund, or did you just open a returns case? If the latter, then you will get a like for like replacement, probably a re-furb. These are usually fine, so I wouldn't worry about that side of things. As far as time goes, Apple turn replacements around pretty fast normally...Within a week is my experience...But a re-fund will probably take longer as they will have to inspect the Mac and test things out.