They should not separate you for non-misconduct reasons if you have a condition that requires an MEB. The Navy takes an odd position about needing to have your MEB submitted and accepted by PEB prior to EAOS/ETS. I think this position is flat wrong and would not stand a legal challenge. (Just as a hypo, so long as you are on orders, lets say on your last day of service, and you are hit by a car and lose a limb, it is very clear that 10 USC 1201, authorizing retirement pay if you are rated at 30% or more, would apply to you. I think the Navy is getting away with murder by separating folks early; Also look at MILPERSMAN sections on ADSEP, most of them have limitations on separation if you have disabilities and/or require an MEB/PEB).
The answer you will get from "official" sources may hew to the party line. However, statutes, case law, and regulations indicate they can't ADSEP under conditions described in your post.