Honestly, I feel if your supervisor is a little understanding, it shouldn't be a problem if you are able to tell him what your long term goals are.
I have seen one of my colleagues get the letter while he was working because he had told his supervisor upfront about his long-term plans about how he wanted to move out of my home country to a place where he could secure his and his family's future in a better way.
In the worst case, makeup something like, you don't intend to move there now but after 5-7 years. Even your manager is not sure if he would be hanging around in the firm for that long.
If it's a big firm you are working for, it's even less troublesome. My company had a separate department that looked into these things. So even fewer people knew about who is doing what.
PS: I got my reference letter addressed to the Canadian Immigration Department. I don't see how you can get such a letter without the issuers knowing how it will be used. Be frank and up front.