Is it legal to upload CC BY papers to academia.edu? Terms of Use are vague on this
If you own the copyright of the paper, which is common for open access papers released under a CC BY license, then you can do whatever you want with it, provided you haven't signed any separate agreement not to do that.  The Creative Commons license is irrelevant, because it's not exclusive: you can distribute the paper under other licenses as well, so there's no legal obstacle to giving Academia.edu whatever non-exclusive rights they want.  (I would never give them the rights they ask for, but that's a personal decision.)

If you don't own the copyright, then you are stuck.  The CC BY license requires attribution for derivative works, and the Academia.edu license does not, so they are asking for more rights than the CC BY license guarantees.  Unless you are in a position to grant those rights (as the copyright holder or through some other agreement), there's nothing you can do.