Was Nikita a bad operative for the section?

Personally, I think she was.

She lied so many times to Michael, Madeline and Operations that her insubordination would quite frankly have got her fired if it were a real job.

Sometimes she lied when it was obvious she should have told the truth - particularly when covering for someone else. And at the end of an episode she somehow always escapes cancellation when it's obvious she should be cancelled (although for storyline purposes that wouldn't be possible to kill off the main character of a show - personally, I believe the Michael character should have been the central character, not Nikita).

She had a problem following the chain of command and was a frequent violator of section rules and procedures.

Also I found her character very conflicted. At times, she seemed very reluctant to kill during missions and at other times she was killing like a serial killer.

I found it hard to like or sympathize with her character as the seasons progressed.