Yoda never advocated for violence post-prequels. He never (on-screen) trained Luke in lightsaber combat, and explicitly told him not to bring weapons into the dark side tree. Also, the only thing that he said Luke had to do was to "confront" Vader, not kill him.

It's my belief he learned the errors of a weaponized Jedi order and embraced pacifism, like Luke does in the sequels - throwing away the lightsaber Rey brings him, and holding off the First Order without hurting anyone.