Granted, we recognize that Cassie's actions are responsible for Tom and Rachel's deaths, but nowhere in the series is that actually acknowledged. The thought never even enters Cassie's mind that it might have been her fault, and Jake quite obviously believes the full responsibility of those deaths lies with him. So, as far as I'm concerned, that does not really count as a blemish on Cassie's record.
And for another thing, she actually does do most or all of the things she says she refuses to. She has taken innocent lives. Not Tom's, perhaps, but she has taken human lives before (most of them morph-capable, towards the end of the series), and I fail to see the difference there.
For the record, Cassie may tell herself her hands are clean of any wholesale slaughter of Yeerks, but keep in mind that when Jake flushed the 17,000, Cassie did nothing to stop him. She even tried to justify it to Erek later by pointing out that "We needed a diversion." A freaking diversion? Might as well have admitted that life isn't so sacred after all. Admittedly not as bad as flushing them herself, but darn close. She's guilty by inaction, given how easily she could have persuaded Jake to spare all those lives.
By the way, please note that I'm not saying that any of these things make Cassie some kind of monster. In fact, I think that most people in a war would make the same justifications and rationalizations as she does. I know I would. It's the only thing you can do to stay anywhere near sane.
All I'm saying is that this kind of stuff deeply and brutally messes with your mind long after it's over. And it's made worse, not better, if you're a decent person to start out with. It's the decent people that are twisted and broken by wars, while the hardened psychopaths are hardly affected at all. Not fair, but it's true.
In the end, I love Cassie as a person, but hate her as a character. I like the things she stands for, and if I knew her in real life I would feel honored to be around her. But as a character she comes off as too good to be true, and thus totally unbelievable.