Lord Dane, yes, as depicted in KOA, the Templars were evil punks. No one disputes that, as it was kind of the point. In reality they, and the crusaders in general, were for the most part, nothing like that.
Also the Pope in Rome had very little to do with what the Crusaders did once they got on the boats for the Holy Land. The Pope didn't direct Reynald on his raids, or the Crusaders to Hattin. The Pope called the crusade, got them on the boats, told them the overall goal, and that's really it. The Crusades were in a spiritual sense, a show of devotion, and an extremely elaborate penance (that's where the forgiveness for past sins (and those committed on Crusade). There were those of course who abused this, and took it as a licence to do whatever they wanted, but that was never the idea.
Also the Crusaders actually just barely won the first crusade. At every turn they faced overwhelming odds, and their series of victories could almost be considered miraculous. The siege of Jerusalem was an extremely hard fought siege, with much death on both sides. A sack of the city was simply standard military protocol for the time. The total exterminations took place on the Temple Mount (the last and fiercest defender holdouts), not the whole city. It was a fierce siege followed by a fierce sack. Nothing abnormal at all for the time. And I would be very hesitant to call the defenders of Jerusalem "not capable". The only reason the siege succeeded as soon as it did (and it needed to, a Muslim relief force was on its way) was because of tactical ploys by the crusader leaders.
Also the Templars weren't around for the first Crusade, being founded almost 30 years afterwards.