I will assume you're using puckel's docker-compose deployment (https://github.com/puckel/docker-airflow) because it's the most popular one and you didn't specify any.
You can share any airflow configuration variable such as AIRFLOW__CORE__DONOT_PICKLE as an environment variable on each of the services specified inside your docker-compose.yml files.
Let's see how that can be accomplish for the scheduler service of the celery-executor version, for example:
scheduler:
...
environment:
- LOAD_EX=n
- EXECUTOR=Celery
- AIRFLOW__CORE__DONOT_PICKLE=True
- ...
...
Each environment value you specify in there will be made available to the service the next time its corresponding docker container gets restarted.