Containers are just a better tool for writing OS configuration scripts. (If your team is full of Chef experts then it's not "better" for your team, but for a lot of teams it is).
What you're saying applies a lot more to microservices, which are a fundamental architecture choice. Containers aren't, they're just better than a tangle of bash scripts which create stateful VMs. And the problems you're describing apply no matter which tools a team uses.
Remember that you can use containers without complicated orchestration or microservices. I think a better argument would be to untangle these three things and describe how each one can solve certain problems or make the problem worse, and under which conditions.