I really dislike Elin and since Ellen is my all time favorite name I too have a major concern about people mispronouncing it or even thinking that Elin is just a different spelling of Ellen! :S
Elin is not pronounced like EE-lin (it's not the correct Scandinavian pronunciation anyway). The pronunciation is more like eh-LIN.
Here's a soundfile I posted on the facts board:
http://www.behindthename.com/bb/arcview.php?id=3272103&board=gen