Fortunately, this should only be a temporary inconvenience. Amazon announced the ability to use EFS with Fargate on April 8, 2020, and an issue in the Cloudformation GitHub repository has been made for the creation of EFS access points through Cloudformation.
We will use a two step deployment until we can unify the process creating the EFS access points for the Fargate tasks with the deployment of the tasks themselves. The first step of our deployment uses Cloudformation to create the necessary file systems, IAM roles and policies, and Fargate tasks and services that do not rely upon EFS for persistent storage. The second step then uses a Python script with boto3 to create the access points for the file systems, the Fargate tasks using the access points, and the Fargate services corresponding to the tasks.
An unexpected benefit has been the simplified Cloudwatch logging afforded by ECS with Fargate. We created a log group in the Cloudformation template and then used that log group within the parameters for creation of the tasks through boto3 with a dedicated stream prefix for each of the tasks. The log group then appears in the AWS on-line console, and the output from each container is found using the stream prefix.
Our experience so far with the Fargate launch type has been positive. We have learned more of the functionality available from the boto3 SDK and simplified the setup of logging from our containers. The deployment process for the access points, tasks, and services is now a single command to run the Python script. Above all else, the transition to Fargate has granted us freedom from concern about the steps required to configure a supporting server instance.