Is there an option to prevent a Job to be automatically restarted after an Instance is restarted?

You could probably get in contact with Safe Support and ask is they're able to change it. I'm not sure how willing they'd be though given every time you get a new instance you'd have to change it again. If it's causing problems though they hopefully they can work with you to reach a solution.

You could try to use an FME workspace itself to modify the configuration file but my guess is that the engine won't have access and you might mess it up breaking the whole thing...heh