Negan loves to punish the innocent for the faults of others, so could he kill Michonne to punish Rick? He could but that’s not very likely.
Negan wants to break Rick and keep him under control but he does have a grudging respect for him. If he really wanted to make Rick suffer he would have killed Carl when Carl snuck into Sanctuary.
Michonne is probably safe. She is a fierce fighter and can handle herself well. It’s not likely that she’s going to die from walkers because she a walker killing machine with her katana.
Although she isn’t a very good shot as long as she her sword she will likely be fine. As she proved after the Governor attacked the prison even when a herd comes at her she can take them out very efficiently.
When it comes to battling humans she’s also extremely capable. There’s always the chance that a random event could kill her, but it’s not very likely. Rick and Michonne, along with Carl and Judith, have the best odds of surviving the entire apocalypse.
That doesn’t mean she couldn’t end up with an iron to the face or some other horrific punishment handed out by Negan if the Survivors lose the war. But even if that were to happen she’d most likely live to fight another day.