Bishop Bishoy asked if some verses of the Qu'ran were introduced after Mohammed's death. Apart from the normal demonstrations held against Copts by Islamists, there has been another much important consequence. Al-Azhar's Islamic Research Council has released an "Statement to the Nation" that openly considers Coptic Christians as Dhimmies who ought to respect Sharia Law to be considered Egyptian citizens:
On Friday, September 24, thousands of Islamists demonstrated in front of Ibrahim Mosque in Alexandria demanding the detainment of Bishop Bishoy and insulting Pope Shenouda and throwing shoes at his photos.
Members of al-Azhar's Islamic Research Council held an emergency meeting led by the institution's head, Grand Imam Sheikh Ahmed al-Tayeb (right), repudiating Bishop Bishoy's comments and accusing him of provoking sectarian tension.
A "Statement to the Nation" was released by the Council on Saturday, September 25 in which al-Tayeb said "This kind of behavior is irresponsible and threatens national unity at a time when it is vital to protect it." He also warned against repercussions these sorts of statements can have among Muslims in Egypt and abroad.
The Statement went on to say the Council stresses the fact that Egypt is an "Islamic State" according to the text of its Constitution, which represents the social contract between its people. "From this stems the rights of citizenship, as taught to us by the Messenger of Allah in his pact with the Christians of Najran, in which he decided that they were to enjoy rights and duties as the Muslims. However, these rights are conditional to respect for the Islamic Identity and the citizenship rights as set by the Constitution."
There are several comments from Coptic institutions about this statement. You can read them on the link above. I'm just going to copy one of them:
Magdy Khalil, head of the Middle East Freedom Forum, issued a press release on September 27, saying the Al-Azhar's "Statement to the Nation" brings us back to the era of Dhimmitude. He thinks this statement, which is addressed to the Islamic nation and Muslims in Egypt and abroad, undermines completely the concept of modern citizenship, replacing it with their perception of an alternative Islamic citizenship, which corresponds to that promoted by various groups of political Islam. "citizenship in the traditions of the Islamic Research Council is conditional to non-Muslims in the Egyptian State by their acceptance of the Islamic State, respecting the Islamic identity and accepting the rule of Sharia," said Khalil, "meaning that the Council has reproduced the unfortunate Dhimmi status as a condition for the Copt to being a citizens in his own country."
He believes the "Statement to the Nation" does not strengthens national unity in Egypt but rather contributes to the increased agitation of the Islamized people, increases the feeling of religious superiority towards the Coptic minority and contributes to the destruction of what remains of the pillars of the civil state.