The Jedi are treasonous! They have attempted to assassinate the Chancellor! They are enemies of the state! Execute Order 66.
On Mygeeto, clone troopers immediately open fire on Master Ki-Adi-Mundi. Ki-Adi manages to deflect the first few blaster shots with his lightsaber and kill a couple of troopers, but was overpowered and shot in the chest multiple times.
On the fungus planet of Felucia, Commander Bly and his men opened fire on Jedi Knight Aayla Secura. Aayla didn't have a chance. She was shot in the back by Bly, then the other troops fired on her repeatedly. Major overkill.
On Cato Neimoidia, Jedi Master Plo Koon was leading an aerial assault against Separatist forces in his Jedi starfighter. His wingmen, led by Captain Jag opened fire on the unsuspecting Jedi Master before he could react. The starfighter turned into a ball of flame, incinerating Koon, before the remains plummeted into the city below.
On Saleucami, Jedi healer Stass Allie was betrayed by her clone troopers when they opened fire on her speeder bike, killing the Jedi Master in the resulting explosion. Not the most honorable way to go.
The clone troopers bear no malice, so the Jedi don't sense their betrayal until it's too late, except for Master Yoda. The best part of the scene is when Yoda takes care of his assassins with sweet a backflip double decapitation.
Related Star Wars Deaths
Episode IV - Han Solo vs Greedo
Episode II - The Demise of Jango Fett
Episode I - The Fall of Darth Maul
Episode VI - A Father's Self Sacrifice