The best thing Lupin ever said about Snape was in HBP, when he gave him credit for the Wolfsbane Potion. But then like the true bystander he is, he added the caveat that he "neither liked him nor disliked him." That is faint praise indeed.
What? What?! WHAT?! He's given credit and praise where it's due to Snape the Potions Master for the Wolfsbane potion - telling Harry in POA that he apreciates Snape making it for him, and adds that he's lucky because it takes a lot of skill to brew. He simply refuses to lie about his personal feelings regarding Snape the man. How does that make the praise less invalid? Appreciating what someone has done for you on a medical basis doesn't mean you have to automatically adore them as a person.
As someone who has medical problems, I can say that I am personally appreciative of every doctor and nurse who has helped me. Does that mean I'm required by some sort of moral law to feel that they're all likeable people? Because I don't.