Embedding is generally easier for the end user, as there is only one file to deal with. It's click and run.
If you embed without encrypting, most players won't know how to get the code and therefore won't go through the effort. It takes only one knowledgeable person with too much time on his hands to extract your code. Then everyone can see it.
If you embed with encryption, you will have to include the key in the export so your program can decrypt your scripts. Most players won't know how to get the key to decrypt the code and therefore won't go through the effort. It takes only one knowledgeable person with too much time on his hands to extract your key and decrypt your code. Then everyone can see it.
So basically it's dealer's choice, but don't stress over it.