I started at this by trying to analyze the legalities, ended up in uncertain territory, and threw that attempt to answer out. Let's take a step back from the question of legality and look at the question a little bit differently: Should you be worried about the exact legal terms at all?
Academia.edu is a startup with an vague and likely rapidly mutating business model. In interacting with such an entity, you should expect the terms and conditions to change unpredictably and without warning. Furthermore, since they are using custom license terms rather than standard, there are almost certainly legal loopholes and potential international issues (there's a reason the CC licenses have so much hidden complexity).
As a user of the site, you are then put in a position of trying to figure out the best spirit of compliance. Regardless of the terms, Academia.edu seems to want to be sharing in the spirit of CC-BY (they seem to basically want to make research information really easy to discover), so it seems reasonable that you could in good faith upload a copy of an open access publication provided to you under CC-BY.
So, what are the likely outcomes of this situation?
- The publisher and Academia.edu's license might turn out to be technically incompatible, but acting basically in compliance with CC-BY, and nobody involved cares about the technical incompatibility.
- The publisher and Academia.edu notice their incompatibility and decide they care, and negotiate with one another to find an accommodation (either peaceably or via legal complaints), in which your action is insignificant, since they wouldn't bother unless a lot of people were doing the same thing.
It is highly unlikely that you would ever end up having a problem because of a good-faith upload to Academia.edu, since to the best of a non-lawyer's ability to reasonably discover, the intent of Academia.edu appears to be compatible with CC-BY, whatever their licensing terms currently say.
Thus, I'd say: it's close enough to be workable; don't worry about it and upload away.