@ Fiona, this situation is very similar to what my husband (a German citizen) and I (non-EU citizen) are going through now.

• He works and lives in Germany, I in Switzerland (non EU B-permit) so we maintain two separate households.
• He does not have a residence permit in CH (German citizen can travel freely to CH) and vice versa (I travel with a Schengen visa to visit him on weekends).
• He reports his marriage status at his city hall and employer, and I do the same here.
• For him, it is a bit of a tax disadvantage because he is considered married but living separately so he has to pay more tax (Lohnsteuerklasse I?). If I were to be registered at his home address, he would pay less tax (Klasse III).
• For me in CH, it is a tax advantage because I am regarded as a single-incomed-married person. Since I don't live in Germany, I don't have to pay tax there.

I don't know if your friend (the husband) would also get a tax advantage if he tells his employer he is married but living separated (due to job situations). But it may be worth to ask the HRD where the husband works.

Isn't there a new tax regulation since 2007 where married couples are no longer "punished" to pay higher taxes than an unmarried person in CH?