I'm assuming, you mean an IAM user with admin permissions for the AWS account and not the actual root user (owner) of the account.
In AWS IAM there is a difference between disabling and deleting access keys. You can disable/deactivate or delete them.
Deletion is final and you'll have to create a new set of keys. The old ones cannot be used anymore and they cannot be recreated.
Disabling/Deactivating keys basically means suspending their usage. They can be reactivated and then used again. If they've been compromised in the mean time, then you'll have active compromised keys. This is a problem.
How secure that EC2 instance is, is another matter. But it certainly is not recommended practice to use access keys on an EC2 instance, especially not keys with such large permissions attached. You should create a dedicated role for the instance and assign permissions to the role with least privileges.
Relevant AWS best practices