As this is an opinion-based question, yours might vary. However, using evidence to support your answer will always be useful.
The Chief felt that McMurphy was gone and he was technically correct in this; lobotomization has serious effects on personality and functionality (most patients are incapable of living independently afterward). In consideration of McMurphy as the representation of life, freedom, and the opposite of the oppressed world in which Bromden lives, it is easy to assume there were no other options. In his way, Bromden was "freeing" McMurphy from the mental prison in which the lobotomy had ensnared him. This action also "freed" the Chief, giving him few personal options but to leave.
In terms of the novel's intentions, Bromden had no choice but to suffocate McMurphy; Ratched's objective in having McMurphy lobotomized was to provide a warning to the patients of the ward--"Don't mess with me..." In killing McMurphy, Bromden made him a martyr for their cause, a symbol of resistance who died in battle.