I had a similar issue and solved it with a patch to ec2.py and adding some configuration parameters to ec2.ini. The patch takes the value of ec2_key_name, prefixes it with the ssh_key_path, and adds the ssh_key_suffix to the end, and writes out ansible_ssh_private_key_file as this value.
The following variables have to be added to ec2.ini in a new 'ssh' section (this is optional if the defaults match your environment):
[ssh]
# Set the path and suffix for the ssh keys
ssh_key_path = ~/.ssh
ssh_key_suffix = .pem
Here is the patch for ec2.py:
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> 'ssh_key_path': '~/.ssh',
> 'ssh_key_suffix': '.pem',
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> # SSH key setup
> self.ssh_key_path = os.path.expanduser(config.get('ssh', 'ssh_key_path'))
> self.ssh_key_suffix = config.get('ssh', 'ssh_key_suffix')
>
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> instance_vars["ansible_ssh_private_key_file"] = os.path.join(self.ssh_key_path, instance_vars["ec2_key_name"] + self.ssh_key_suffix)