Why does Takuto break Wako's seal at the end of Star Driver?
It was because he wanted to save Sugata

Sugata wanted to seal Samekh with him forever, meaning he wanted to sacrifice himself. And Takuto wanted to save him, that's why he broke Wako's seal. Takuto's only chance of saving him was to break Wako's seal to unseal the Zero Time. Wako wanted to save Sugata as well that's why she allowed Takuto to break her seal, agreeing both without a single word (which was just amazing for me!). 

I hope I answered your question clear. This is purely based on my understanding of the ending. :)