That's not really what Aminator was intended to do. Rather than create a snapshot, you could use the ec2-create-image (aws ec2 create-image from awscli) command to create an AMI directly from a running instance.
If you choose the snapshot route, depending on the OS, you could possibly quiesce the filesystem prior to snapshot and unfreeze it once the snapshot command returns. Linux has the 'fsfreeze' command for doing that sort of thing (on ext3/4, xfs, reiser, and jfs), and you can use something like dmsetup to freeze/unfreeze a LVM volume if that's in play...
That'll ensure the snapshot you've got is consistent and you can safely turn it into an AMI at a later date w/ ec2-register-image.