"The Muslims may have treated non Muslims as second class citizens, but they left them alone."

What 'Muslims' are you referring to, here?  

The fanatical Berbers that terrorized northern Africa under the Fatamids and expanded the caliphate by force, using 'convert or die' methods everywhere they went?  The Mamluks that inherited the Abbasid caliphate after the Mongols ran it over and who were slaves converted by force and turned into fanatical soldiers by the Abbasids?  The Turkish Ottomans who shifted the caliphate towards harsh, orthodox Shia beliefs and actively persecuted other religions, including 'heretical' branches of Islam?

The era you refer to is really just the flowering of the Abbasid caliphate around Baghdad, and it lasted maybe 200-250 years.  

"The Catholics also wiped out Islam and Judaism completely in Spain, Portugal and Italy during the Inquisition."

I love how you leave out the Muslim invasion of the region totally from your narrative.