Did the Germans respect neutral embassies in the numerous European capitals they captured? Did the Allies respect neutral embassies in Rome? Did the Soviets respect neutral embassies in Berlin?
I'm not qualified to answer your question, but could you clarify what you mean by respected? Do you mean not looted?
According to the website of the Swiss Embassy in Germany, during the battle of Berlin, their embassy would be the only building left standing on the Spreebogen, which is why the Soviet side used it as rallying point for storming the Reichstag.
For the time being the staff was moved into the embassy's bunker.
Source: Homepage of the Swiss embassy in Berlin
After the war the "Swiss embassy" would be located in Bonn in West Germany. Due to the Hallstein-Doktrin until 1969, West Germany boycotted and put economic sanctions on all states which recognized it's Eastern counterpart. Thusly there would only be a Swiss "delegation" in East Berlin, no "embassy".