Hey Holger!
This is a great question.
One of your best options is to create separate URLs for each language as recommended by Google's documentation regarding multi-regional and multilingual sites found here:
http://support.google.com/webmasters/bin/answer.py?hl=en&answer=182192#1
example:
1. www.website.com (english)
2. www.website.de (german)
This would be a lot of work and (potential) site restructuring so how viable this option is would be something you would need consider.
Another option is to create a subdomain for the english site (e.g. http://en.website.de). Once this is done, you can start a campaign for both website.de and en.website.de. This way you can isolate just the english version of the site.
The last option that I can think of would be to create a campaign for your main/originating domain. If the english subfolder is housed on that domain, we'll more than likely crawl it along with the rest of the site. To separate out the English and German content, you could just filter/remove it from an exported CSV report.
Regarding your suggestion for excluding folders and URLs, this would be an excellent feature request. I recommend submitting this in our feature request forum. Our Product team checks this daily and uses it to help plan out our roadmap for future releases and may add this in there.
Hope this helped clear things up and let me know if you have any other questions. Thanks!
David Lee
SEOmoz Help Team