What is being done in the name of Islam

From the New York Times

The American military attacked a mosque in this holy city on Tuesday in its largest assault yet against the forces of the rebel Shiite cleric Moktada al-Sadr, even as the first signs emerged of a peaceful resolution to the five-week-long standoff with him.

Now that the cleric is being shunned by the Shiite leaders and community and his followers are being killed by the US and Iraqi forces, al-Sadr is interested in making peace.

But why are Muslims willing to let this person who is acting in the name if Allah defile the mosques and the Shiite holy cities by storing weapons there and using the mosques as military bases? Wouldn't the devote Muslims be demanding al-Sadr leave and either stop calling himself a Muslim because Islam is a religion of peace or to stop his actions which are bringing dishonor to the Prophet and the word he brought? Of course if al-Sadr is acting as a good Muslim should act, then we do have a war of religions as well as culture and it will be the world against Islam.

Can someone, anyone please enlighten me?