When you log in to your machine via AFP or any other service you inherit the permissions of the user you log in as. I think that is the problem you are running into.
As far as security goes, under AFP your password is hashed, and there is an option to encrypt traffic (at least there was under Tiger) but otherwise all other data being transferred is unencrypted. If you want encryption, your best bet is to either look into SSH tunneling, or using SSHfs/FUSE to connect to your machine remotely (the latter is what I do, performance is also better this way).
I hope this helps!