Protecting against "swapped devices" is simple: put a secret key in the device, ask it to produce a signature, check it with the public key. Any device other than yours won't know the secret key.
I'm not sure what attacks you refer to when you say "malicious program-binaries". I'm having trouble imagining something fitting this description which is thwarted by the vendor blowing the programming fuse but isn't thwarted by you blowing the fuse yourself.
I'm not sure what attacks you refer to when you say "malicious program-binaries". I'm having trouble imagining something fitting this description which is thwarted by the vendor blowing the programming fuse but isn't thwarted by you blowing the fuse yourself.