My negativity doesn't have as much to do with Clark's actual actions this season, but the way she was written overall, and the way that other characters were written when they were around her. From the start of the season, all of the other characters virtually lost the ability to think for themselves when Clarke was around them. She was the only one who seemed to be right all of the time and the only one who seemed allowed to come up with solutions to their problems (at least the finale was consistent with this, the thing that I hated the most about this season). I think the show spent too much of this season forcing Clarke into situations that would turn her into a darker character, often to the detriment of of the other characters (their characterization) and to the overall plot. The show really seemed to have a tendency to make other characters behave inconsistently or out of character in order to force Clarke's character development.
First there was the whole thing with Finn. I'd never really liked the character much. Going into this season, I considered him a poorly developed love interest with very little depth. His PTSD, or whatever, seemed to come out of nowhere. During the first couple of episodes he's acting perfectly rational, urging Bellamy to keep his cool and being really supportive of Raven. Then a couple of episodes later, he's executing a Grounder and later on murdering 18 innocent people. But I felt that it was an interesting enough storyline, and it felt like the show was finally going to give him some depth. Then, while he was just starting to get that depth, the show made it so that the Grounders would settle for nothing less than his death in order for there to be peace between the two peoples. Kane said, that based on his time with Lexa (barely none of which was shown), he thought her to be a reasonable person who might settle for a trial and imprisonment, but then they had Lincoln tell everyone that the Grounders would never accept it, even if Lexa wanted to, because by their custom/law blood must have blood and Finn had to pay for the deaths of those 18 people. Indra was the loudest voice calling for Finn's blood and she hated the idea of dealing with the Sky People after what they'd done, even after they promised to cure the Reapers (and they killed far less people than the Mt. Men). So Finn did the right thing and turned himself over to the Grounders even when all his friends were still trying to protect him. This forced Clarke to kill Finn out of mercy, in order to spare him a horrible death at the hands of the Grounders. I didn't really mind Finn dying much, because he was my least favorite character and it seemed to be leading to something more.
Clarke had to make a terrible decision, she started to see love a weakness and everything. She became a darker character. Kane faded into the background and became near mute, even though he was the one who went to negotiate with the Grounders earlier in the season. He wouldn't even take back the Chancellorship when Abby offered it back to him. Jaha became mentally unstable, was imprisoned for a bit during the Finn ordeal, and then left for the Promised Land. Abby seemed to be basically forced to remain Chancellor because she was Clarke's mom, and that gave the show a decent reason for how Clarke was allowed to play leader and do whatever she wanted.
Then the whole missile strike happened. Clarke convinced Lexa to leave and not to warn anyone from the village. They made a big deal about how no one could find out about what they did because it would ruin the alliance. Lexa even wanted to kill Octavia because of it. Lexa used the missile strike to further motivate the Grounders to get revenge on Mt. Weather. Everything looked to be building up to something big.
Then they get to Mt. Weather and after a little bit of fighting, Lexa decides to take a deal to retreat. It would have been ok if there was some sort of fallout from her decision, some kind of payoff to everything that came before, but there was really nothing. So much for "blood must have blood", and that Lexa can't do whatever she wants and has to answer to her people who would demand justice/vengeance. I guess Clarke feeling the sting of betrayal (and later being forced to kill all of the Mt. Men) to further her character development, was more important than anything else previously established on the show. The 18 people that Finn killed and needed to die for, was a bigger deal than the 250 people that died in the missile strike and everything else that the Mt. Men did to the Grounders, because it was more relevant to Clarke's character development. At least they had Indra leave Lincoln the knife so that he could make the choice to help Octavia and get Cage. The whole deal and retreat seemed even sillier during this episode, by how easy it seemed to get into Mt. Weather and kill everyone, all without the Ark people losing anyone important (even though the show put all of the important Ark characters in danger).
Now, some of the way that the Grounder storyline played out, could have been due to the actress playing Lexa being unavailable for the finale (I think). The showrunner mentioned in an interview, about last episode and Lexa (that I read and need to find again), that he apparently didn't want her to die during the finale because Clarke wouldn't have gotten a chance react to her betrayal properly (or something along those lines). That secrets were still out there and how Clarke dealt with what happened with Lexa would part of next season. But again, even if they're going to deal with it next season, Clarke's character development comes across as being more important than consistent characterization for other characters and telling an internally consistent story this season. Hopefully next season doesn't handle Clarke's character development in the same (heavy-handed and contrived) way as this season.