There may be some setting for fckeditor to tell it not to enforce strict xhtml which might allow it to use the target attribute though the content will be invaldi as far as the w3c validator is concerned. In the post you linked I was talking about the links module feature not links directly created in fckeditor. For that feature I implemented support for new windows using the onclick event of the link and a little javascript like this:

onclick="window.open(this.href,'_blank');return false;"

You could do that also using the source view of the editor though its rather awkward for non technical users.

Myself, I prefer to follow the standards and not open in new windows but instead train my users that they can be and should be in control over opening new windows. All they have to do is right click the link and they get an option to open in a new window or new tab. This is the reason they deprecated the target attribute is because all browsers support opening links in new windows and its better to empower users to be in control rather than taking control away by opening windows for them automatically.

Best,

Joe