There are some points where Cassie's refusal to be morally dark helped them out. For example she didn't kill Aftran as essentially everyone else wanted to do and though Aftran says that there are other yeerks who don't want to enslave it seems it was Aftran itself that organized them into the resistance. Later, one mission where Cassie refuses to participate due to the imorality of what they're doing she ends up saving everyone by going against her own morals and attacking other humans, if she'd just gone along and been morally dark both the Animorphs and the Yeerk Peace Movement could have been wiped out.
The problem isn't so much Cassie's morals as it is the effects they have, she's pretty much always proving that doing the right thing will be rewarding in the long run . . . except at the very end of the series, and even that's debateable. In reality, unless you want to get religion involved there's little evidence that doing the right thing will always (if indeed ever) have its own rewards later on.
