The Kids Next Door's injury policies seem to be a way to justify Cree staying as a hero, but it actually does make a fair bit of sense for several reasons if one thinks about it.
Considering how many operatives try to betray the Kids Next Door or run away from their decommissioning, threatening the same to someone who had their life permanently changed in some way not only makes it obvious those people would turn traitor if given half the chance, but also makes the KND look much less heroic if they did try.
Since decommissioning erases all memory of being a Kids Next Door operative, this would include the accident that crippled the operative in question. Letting someone who was crippled keep their memory avoids any unwanted questions.
Cree, with her injures, is considered to be a school outcast, yet is still able to pick up on a lot of Teen Ninja plots. A crippled operative would be a perfect spy as not only would they fly under the radar, they'd also be underestimated if anyone did notice them.
In addition to her injury resulting in her no longer being threatened with decommissioning, there's another reason Cree stays heroic as a commentor pointed out. Namely, she (seemingly) knows what being betrayed by someone you trusted at a crucial moment feels like and likely didn't want to put anyone else through the same pain.
