Well, an embassy usually have some kind of diplomatic immunity to grant them legal immunity from the jurisdiction of another country's laws. So certain packages cannot be searched and some actions are excluded from the host countries laws and regulations.
Now, I wonder if this is extended to the "currency" being used in those countries where Bitcoin is banned. How would an embassy benefit from using Bitcoin, in a country where it is banned? (They cannot use it as legal tender... so what can they do with it?)
But this is done in advance to accepting the embassy. The host country has every right to reject the embassy from establishing their own rules they still need to be accepted by the host country. That is why some embassies in the past have been forced out of the country because the new government does not agree with their own rules. This happens every couple of years so it is not like it has not happened before. Now, I wonder if this is extended to the "currency" being used in those countries where Bitcoin is banned. How would an embassy benefit from using Bitcoin, in a country where it is banned? (They cannot use it as legal tender... so what can they do with it?)
But yeah, good choice on picking the first country to do this. They know that Switzerland is the center of finance, and where most financial innovations start. The Swiss government wouldn't really mind about bitcoin in El Salvadorian embassies so long as they do not go over the said territory. 
