Get authoritative immigration advice from a good immigration attorney before you do anything.
A D-1 is a non-immigrant visa. Marriage to a US citizen is considered 'immigration intent' and can lead to a denial of entry. Also, these crew visas are a special animal in that there are restrictions on whether you can change into a different status or not.
In order for her to stay here, you will have to get permanent residency for her. This occurs by filing form I130 with either your local USCIS office, a central processing center or with the US consulate in germany. After that, she can obtain an immigrant visa for the US and enter on that to obtain a green-card.
Her citizenship will not be affected by obtaining a green-card (her tax-status however will, get good tax advice here) Only, if after 3 years of residing permanently in the US she CHOOSES to apply for US citizenship, this will become an issue. At that point, she would have to decide whether she wants to maintain german citizenship (by applying to the german goverment) or she would loose it (by default) if she assumes US citizenship.
