Ah. The question of security.
I think the question you should be asking here is what do you do with say, for example mySQL passwords in your php config files?
To be quite frank, I would say that if someone managed to get a copy of your files, then your security needs rethinking anyway. For my own use, I generally only keep the passwords in one place, (on the server where they should be used) and make sure that I use a randomly generated password each time (paste it into the config file, and voila!)
To be honest, if it's not your own host, ANY sensitive data can be compromised.
If it is your own host, I'd suggest using proper permissions within Linux, and PHPSuExec to make sure that only the scripts that YOU write can access the files.
Anyway, to answer your original question, your AWS Access / Secret Keys are just the same as a MySQL password, Ok, it has the potential to let someone access your service, but it doesn't give them access to your personal details. Even with symetric encryption, if your script has a security hole, the information can be accessed.
Put simply, you take a risk when you put these keys anywhere that is accessible to anyone but you. How much do you trust Amazon's servers not to be compromised?
My suggestion would be to try and add as much security as you can, but keep an eye on your account, I'll generally have a cron job running to send me an email with changes to my S3 account (new files uploaded, new buckets etc etc) and from that I can tell what's going on.
There is no easy solution, it's a mix of securing each seperate layer of the System. I mean, if you use symetric encryption, the password for that has to be stored somewhere, right? or are you going to type it in every time ?
Hope this helps