All clones had chips, so why didn't the Jedi and remaining captains knock out the clones and take out their chips instead of killing them like Ashoka knocked out Rex in The Clone Wars and took out his chip.
The Jedi didn't know the purpose of the chip, and most of them didn't even know about its existence.
Only Palpatine/Sidious, Dooku/Tyranus and the Kaminoan scientists were aware of its existence and more importantly, its purpose.
During The Clone Wars (S6, Ep 1-4), Fives discovers the existence of the chip and its purpose. He tries to warn both the clones and the Jedi but is killed, in front of Anakin and Rex, before being able to explain everything he discovered.
Shaak Ti and Anakin become aware of the chip during this story arc and report to the Jedi Council, but even then the Kaminoan scientist and Palpatine explain that the chip is harmless and the incident regarding Fives was due to a parasite. Thereafter the Jedi ignore the true purpose of the chip.
When Order 66 is issued, Rex says "Find Fives" to Ashoka, referring to the chip discovered by Fives himself. While Rex and Ahsoka have a clue about the chip and its purpose, other Jedi simply ignore it.
On top of that very few Jedi survived Order 66; the clones were able to slay them. (As shown in Episode III: Revenge of the Sith where even members of the Jedi High Council such as Ki-Adi-Mundi and Plo Koon are overwhelmed by the clones.) Knocking out all the clones and removing their chips would have been a nearly impossible mission due to their numbers and fighting ability.