I'd assumed that he was scarred, or was having a severe allergic reaction.
Whatever way it is played, it will obviously be a plot point, and still think for maximum shock value, though at this stage there has been so much shock, they will go for the reveal from the original books.
Season overall was very good. I'm still interested in the next season, and though i'm not a fan of gore, i think that the writing and some of the very sharp, pointed messages the show is trying to convey and get across will have me sat watching this next season.
From way the season was left, are we now literally at Issue 1? The status Quo seems to be set for them to now be working for the Government, and perhaps time they were "upgraded."