I was recently struggling with a similar issue.
Encodings out of Mail.app are, apparently, a mess. Mail.app is handling the encoding correctly internally and, using drag and drop, you can get text in the proper endcoding (content is always in UTF-8, it seems), but if you save the text or transfer it via AppleScript, Mail goes on a wild randomization spree and you can’t be sure of exactly what you will get.
Although I figured out a solution to my particular issue (with Wolfgang’s help), since it uses the content of the message and not the source, I don’t know if it will work for you.
That said, while I was struggling with the Mail.app issue, I also looked at various other e-mail clients. The state of Mac e-mail clients is pretty all over the place. But, one constant seems to be their lack of good AppleScript support.
The one exception to that I found was Outlook (Outlook 2011, not the subscription-only Outlook that was just recently released, which I haven’t tried). Say what you will about Outlook (it is overkill for what most people actually need, has several interface attrocities and can be buggy in may different ways), but it has an incredibly rich AppleScript dictionary and it’s handling of encodings seems to be rock-solid. I was able to use it during my battles with Mail.app without having to change my Xojo application at all, and it worked very well.
It’s entirely possible that Outlook 2011 is not an option for you, but I wanted to throw this out as a potential solution, just in case.