It's good that you have some ideas but Clover is not really a character that starts out good and turns bad. She is more of a figure representing loyalty and goodness - much like Boxer. She fulfills a motherly role on the farm.
Now consider the fact that Animal Farm is an allegory and there really is a message Orwell wanted to share. Orwell was frustrated by the fact that, despite being oppressed and initially fighting for justice and to establish an ideal, people - or in this case animals - allow themselves to be manipulated by a different corrupt force.
Clover knows that things are not what they seem but, due to being a trusting and not well- educated being, feels powerless to do anything. Everything she questions is explained away. Even though, she does not completely trust the explanations given to her, she cannot argue with Squealer. For example,
No animal shall kill any other animal
No animal shall kill any other animal without cause.
One possible metaphor would be to describe Clover as an abuse sufferer who stays in a relationship - for the sake of the children - in this case the other animals. Abuse sufferers usually continue the cycle and having been abused before, they willingly enter into new relationships that slowly but surely repeat the cycle of abuse. Abuse sufferers, at first, accept the explanations of the abuser and believe in the inherent goodness of their abuser. They either forgive or just allow things to disintergrate slowly.
The animals were abused under Jones' 'rule' and now the pigs are deceiving them, slowly introducing a class system of their own, having used the animals to defeat the common enemy. The gradual warping of the Commandments defeats the purpose and intent of Animalism.
This metaphor would suit Clover in view of her position as a motherly figure who would always strive to do her best for her 'children' but there comes a point for an abuser when his or her best is actually not good enough! Without support an abuser often becomes apathetic and rather simply survives.