Is it permissible to spend money acquired from a scholarship, which was not deducted for days of absence despite warnings to that effect, on charitable causes?

You must adhere to the contractual terms specified by the Ministry, based on Allah's saying: "O you who have believed, fulfill [your] contracts," and the Hadith (definition): "Muslims are bound by their conditions." What you and your friend did, signing for an absent person, is impermissible because it violates the terms and involves lying and deception. Therefore, you both must repent to Allah and return the portion of the salary corresponding to the days of absence to the Ministry. It is not permissible to spend it on charitable causes if returning it is possible.