Eidolons are summoned creatures, they have their summoner's alignment. Protection from _____ would stop it from being able to attack with natural attacks (unless he has SR). The guy with the protection can't do anything offensive directly to the synthesist, but he can totally ignore the nat attack onslaught and go about his business.
That and any other spells that deal with outsiders (the synthesist gains that type) or dismissal type effects that target extraplanar creatures.
