Agreed that Blackwater deserved the win. Now, I'm not too knowledgeable about the Hugos, but does DW always split the vote between its own episodes every year?
If I remember correctly, the Hugos use Instant Run-off Voting. If nothing gets past 50%, then the lowest vote getter is dropped and second-preference votes are counted. This continues until something crosses the 50% threshold. This minimizes the problems due to vote splitting.