Question
Why were they allowed to light a fire on Shabbat in the Temple for the sacrifices if the Torah says not to light fire on Shabbat?
Answer
That is not the only Shabbat prohibition allowed in the Temple. Another example is the actual slaughtering of the sacrifices. In addition, the High Priest would wear Shatnez-a garment with wool and linen, normally a forbidden material. Since the Temple laws are specifically prescribed in the Torah, there is obviously no problem regarding Jewish law.
Perhaps we are meant to understand how special the Temple is. As the resting place of G-d’s presence (The Shechinah) in this world, many of the prohibitions are suspended for the purpose of the Temple service.