Let me first start by saying that neither Snape nor Slytherin House are evil. After all we are all here, right? Secondly, I was under the impression that in order to be a Head of House you had to come from that house to begin with. I'm not sure, but I think that Snape is the only Slytherin on staff. So he has to be Head of House. Also, by placing him as Head of House, it helps him as a spy to get information for Dumbledor. Gossiping kids of death eaters make great informants.