I’m afraid that I don’t know exactly what is stored in a Google reader backup, so I don’t know whether it includes the full text of all past articles, the full history of all feeds; but not the articles themselves, or just a list of feed URLs, and I don’t know exactly what Akregator can do with one. Akregator definitely has an ‘import’ feature(and an ‘export’ one); but the devil is often in the details with such things. (It seems a hopeful sign that ‘OPML’ is mentioned in a few articles about Google Reader exports, and is also Akregator’s native import/export format; but there’s compatible and there’s “compatible”)
If you have a Google Reader backup with enough contents to be a meaningful test(doesn’t need to be your ‘real’ one; but obviously has to have some stuff in it) that you wouldn’t mind me seeing, I’d be happy to give it a shot and tell you what it does and doesn’t do; but your specific migration trajectory is not one I’ve faced personally, so I can’t comment in detail, I’m afraid.