On Daf 20a, the Gemara says that the Cohanim were permitted to light the fire before Shabbat in the Beit Hamokad because they were very careful and wouldn't come to adjust the fire on Shabbat. My question is: It seems that the Gemara had a much simpler heter for the Cohanim to light the fire before Shabbat. Why didn't they just invoke the rule of "Ein Shvut bamikdash?" There would be no hava amina to say that it shold be assur since the whole issur was based on an issur d'rabbanan which would not apply in the Bet Hamikdash.
Very good question. It seems that we find a number of prohibitions of "Shevus" on Shabbos that do apply in the Mikdash (as TOSFOS points out later on 123b, DH Lo Sidur. It is a question, though, why Tosfos did not prove this from our Mishnah, as you suggest!).
Perhaps since the Beis ha'Mokad was half Kodesh and half Chol (Yoma 16b), the reason of Ein Shevus ba'Mikdash does not apply.