Later in this chapter Jesus says, "He who does not believe is condemned already" (Jn 3:18). Almost no one thinks that all people (including infants and the severely retarded) who die without personal faith are consigned to hell, yet we do not conclude that Jesus was not really talking about faith. There are two issues here: whether a statement is meant literally and whether it is meant absolutely.
Virtually everyone allows that some who have not been "born of water and Spirit" (however that is understood) may still be saved. You probably allow for "exceptions" yourself. You have not escaped this difficulty, only compounded it by concluding that Jesus is talking about something other than literal water. (Notice the context, by the way: Immediately after Jesus’ speech, the disciples go about baptizing [Jn 3:22].)
The same reasoning applies to Jesus’ statements in John 6 about those who do not eat his flesh and drink his blood having no life in them. The question whether the requirement is absolute is distinct from the question whether it is meant literally. In short, both baptism and the Eucharist are normatively necessary for salvation, but not absolutely necessary.