When Clover thinks, "But still, it was not for this that she and all the other animals had hoped and toiled," she expresses disappointment and realization that the initial ideals of equality and a better life for all animals have not been realized. The current state of affairs goes against the original aspirations and efforts of the animals.

rephrase as a 9th grader

Clover feels disappointed and realizes that the animals' hopes and hard work for equality and a better life have not come true. The way things are now goes against what they originally wanted.