Heh, this is the most I've seen you write outside of review replies, Ou-Rex.
Having a good guy die doesn't make something dark - look at Gurren Lagaan. Sure, Simon went into a pit of despair because of it but it only lasted an episode and it was right back. There might be dark chapters or darker stories tied into the main story but having one or two incidents doesn't shift the overall direction. As for Tsukune getting injected, it was treated as a power-up but the power-up came with a warning and there was always the fear that something could go wrong - and then it did.
The entire arc with the Outcast Ayashi was the darkest arc - even compared to this one. For me, it's because it happened while at the school and it was also when Tsukune was in danger of losing more than his life - his very sanity and personality, which the girls adored him for. There was the very real presence of danger in that time, not only to Tsukune, but to the other girls as well because the danger was so close (within the school).
But (thankfully) Ikeda loves comedy so he's kept it from getting too serious by putting some stuff in now and again. I mean, really Ruby...?