Is there a way to run initial SQL when creating an RDS database instance using CloudFormation?

No, it's not possible. However, you could have an EC2 instance connect to your RDS instance to do it. I'd probably store a .sql file in S3 and use a cloud-init script on the EC2 instance to download the file and execute it.

It would also be possible to create a CloudFormation custom resource. There is a good discussion about how to build one using SNS here; it is also possible to build one using Lambda. Custom resources are essentially just RPCs, so it wouldn't be difficult to create one to initialize a database with a schema, for example.

CloudFormation still doesn't hold any solutions for us, but hopefully they will add Database Migration Service support soon.

In the meantime, there is great solution if you're using CodePipeline: create a migration stage that invokes a Lambda function to run your migration. I stumbled across this guide for invoking Lambda from CodePipeline that may be helpful for those unfamiliar.