This post was edited on August 10, 2014, for better spacing and ease of reading.
Kerrigan’s actions in StarCraft II, especially Heart of the Swarm, are all over the map. Her moral standards change hourly, ranging from a mentality of slaughtering everybody one day to trying to spare as many lives as possible the next.
The first glaring point would be when she attacked Kaldir. Apart from the fact that everything she needed there could have just as easily been acquired on a planet without a Protoss presence, she launches a bloodbath that sees every Protoss perish. The only motivation for this given in the game is that Kerrigan feared some vague Golden Armada. The armada in question never came for her before, so if she simply kept her location hidden until the Swarm was restored, there would be no reason to expect it to do so again.
In any case, there was absolutely no point to slaughtering the Protoss who tried to flee in the final Kaldir mission. If they were out of communications range with Shakuras, then they were at a considerable distance from it that would have taken a great deal of time to cross. Kerrigan had no need to silence them even if she feared that Golden Armada, because they would not reach Shakuras in time to make any difference. Despite that, she chooses to kill them all anyways.
Another problem is what occurs with Warfield’s army on Char. She offers him the chance to flee, which he refuses out of the justified expectation that she would not hold up her end of the deal. Kerrigan subsequently slaughters his entire army, even though she had no real need to. When she wipes out his army, she finds Warfield trapped in his operations centre, mortally wounded. She kills him, and then spares a single transport filled with soldiers, apparently out of compassion.
If she actually wanted to spare lives, she could have done so much more effectively. Leaving Warfield on Char, for instance, would not have done any great harm to her cause. She could have simply re-established the Swarm on another planet and left Warfield to sit there until such time as she dealt with Arcturus. He was largely stranded there in any case, since Kerrigan had destroyed every one of the Gorgon Battlecruisers he had wasted so stupidly. Trying to kill him off on the spot would only waste some of her own forces, especially since Warfield was willing to nuke his own base, and the Swarm would need everything it could muster to assault Korhal.
One especially severe flaw to note is what she does with the various Broodmothers who contact her throughout the story. She tells them to attack various Dominion industrial worlds producing war materials and raze them to the ground, leaving no survivors. This is an incredible way to waste valuable resources that could be used on Korhal, as those industrial worlds were irrelevant in the type of war she was waging.
If she was fighting a war of attrition over several years, they would certainly be important targets. However, the whole of Heart of the Swarm takes place within a few months at best, which means she was planning a lightning strike. Such a strike deals with the forces already in place, as such a short timeframe means that production capabilities would be largely meaningless.
The burning of so many inhabited worlds is also in stark contrast to what she does later on Korhal. She goes so far as to handicap her own assault by landing outside the city, and later in avoiding civilian-heavy districts, in order to give Valerian time to evacuate civilians from the city. What she did would have weakened her attack greatly over a few million lives.
On the other hand, she showed no signs of compassion or doubt over ordering the destruction of numerous worlds with millions of inhabitants apiece. It should also be noted that all of these consequences were utterly ignored by Blizzard, which simply threw the references in without any kind of follow-up, so it would not be terribly surprising if Legacy of the Void proceeded to ignore that destruction and allow Valerian to miraculously repair the Dominion in time for some final showdown with Amon.
The ultimate problem with Kerrigan’s morality and choices is incredible inconsistency. Her actions simply make no sense, as they veer wildly from plans for massacres to compassionate deeds, sometimes combined at the same time. If she was intended to be written as a redeemed person to some extent, the industrial worlds should never have come into play, and the Kaldir attack would not have had a good point to it. If, on the other hand, she was to be shown as somebody who was offered redemption and turned away to commit further evils, she certainly should not have sabotaged her own goal of deposing Arcturus by crippling her attack on Korhal.