It was (strongly) suggested by more than one person while I was writing this that I end it happy, to balance out all the fucked-up-ness. So...here's a hint at happy. Looks like Snape and Harry may be able to bury the hatchet, and hopefully not in either one's back. But yeah, I think it would be a slow process for them to fully change their attitudes towards each other, hence Snape's parting shot before the close of the fic.
Snape was quite protective of Lupin, yes, but no more than Lupin was of Snape. They both took credit for being the cause of all the bad things, and pleaded (well, Remus pleaded while Snape strongly insisted) that Harry not hold anything against the other. Snape will never tell Lupin about the stew, though. It was probably difficult for him to tell Harry, since the fewer people who know, the less chance there is for Lupin finding out. He had his reasons for telling Harry, though, and they outweighed the potential risk.
Thanks for reading, and I'm glad you enjoyed it! ^_^