I am only seven or eight episodes into Princess Tutu, so what I say is based on speculation perhaps wholly unrelated to the actual telling of the story.
Princess Tutu had gathered two pieces of Mytho's heart, loneliness and fear. An unfeeling person who suddenly feels only loneliness and fear is in bad shape. Mytho understandably comes to fear Princess Tutu as someone who brings him only pain and suffering.
Princess Tutu goes through a crisis of faith, wondering whether her attempts to return Mytho's heart are actually beneficial to him. Seeing the pain she has caused, and hearing him explicitly cite her as the source of his pain and fear, she resolves to give up. However, when she sees him in danger, she once again comes to his aid and he reveals that he wants his heart back, despite the pain. It is as this point that Fakir (especially) and Rue step up their attempts to interfere with Princess Tutu's plans (though, initially, not explicitly; they desire to keep Mytho's heart broken and scattered).
Rue is a terrible person. She loves Mytho but in a manner so twisted I shudder to call it love. Instead, she desires Mytho as an object; she actively fears the thought of him possessing a heart and exhibiting feelings, even feelings of love for her. She wants a puppet, a plaything, just a body that she can utterly control. One wonders whether she is more fearful of emotional intimacy or more desirous of control over another human being. Separate from her psychopathic interactions with Mytho, she is also the villainous magical girl Kraehe (which I am guessing is German for crow or raven).
Fakir's motivation is not as transparent, initially. He has all the trappings of the evil stepmother who locks Cinderella away "for her own good." You get the simultaneous vibe that he cares for Mytho (trying to protect him) and does not care for Mytho (has no qualms with hurting him or cloistering him in his room). His reaction to Mytho regaining his heart is not the disappointment, fear, and hatred of Rue but a fear that something bad will happen, something larger than Mytho.
Princess Tutu and Fakir faced off in the last episode I watched. Fakir wielded a sword that could shatter Mytho's heart again but failed to land the blow. Mytho, too, tried to dispel his fractured, hurtful heart but Princess Tutu convinced him to bear the pain until the rest of his heart returned.
This is where my rumination starts. The backstory of Princess Tutu is that the Prince (Mytho) fought against a demon raven. In order to seal away the raven, the Prince had to shatter his own heart with a magic sword. So Princess Tutu is unwittingly acting to free the demon raven through her kind and loving attempt to return Mytho's heart while Fakir is consciously acting to keep the raven imprisoned by opposing her. However, while Fakir may well know the history of Mytho's shattered heart, Princess Tutu seems ignorant of it.
In the past, as the Prince, Mytho chose to shatter his heart. He knew that was the only way to keep the demon raven sealed in its prison. Now, heartless and ignorant of his own past, Mytho consents to Princess Tutu's aid. However, as the Prince Mytho entrusted his well-being to Fakir. Fakir's duty is to keep Mytho's heart shattered; Mytho freely chose this fate for himself and asked Fakir to maintain his heartless state for the good of all. So the question is, which of Mytho's choices should be honored? Can he change his mind while ignorant of his past choice and absent his heart? Is Fakir justified in countermanding Mytho's current choice in favor of his previous decision? If informed of the past, of the demon raven and Mytho's free will decision to shatter his heart to imprison it, is Princess Tutu justified in returning his heart to "make sure that is still his choice"?