I still think there is a gap here in the different ways we are understanding the events. Where are you reading that he amassed some huge army? Where does it say that Muhammad went in and forced people to convert? Where are you getting this from? It seems like every paragraph you list you are siding with the bad interpretation of events. Muhammad was in Mecca preaching to his people all those years, and just like Jesus, they tried to kill him. But, Jesus was more violent in those three years than Muhammad was.
Your expecting that Muhammad should just let people choose their beliefs, while everyone is getting persecuted and killed? It seems to me that one of Muhammad’s missions was to end the persecution and killing so people could then choose whether or not to follow him.