I think killing Boone badly harmed the series because the Boone and Da'an friendship was the best part of the first season. You can't get rid of the best part of your show and expect to recover from that.
Except that Da'an's character was profoundly simplified in the second season, so the Da'an we knew in the first season pretty much ceased to exist too. Even if they'd kept Boone, the change in the sophistication of the writing would've ruined that relationship anyway.
But it didn't have to be that way. In a late first-season episode -- the second-last one, I think -- they started to set up a Lily-Da'an relationship that could've taken the place of Boone-Da'an if they'd done the smart thing and made Lily the lead after Boone was written out. That could've been interesting -- if the writing had remained up to par. Which, sadly, it didn't.