(a) Many Rishonim learn that the Kodshei Bedek ha'Bayis are redeemed by anyone who wants to redeem them, and are not destroyed (see Rashi 111b DH "mi'Kan" and Ra'avad Hilchos Avodah Zarah 4:13). However, the Rambam (ibid.) does indeed learn as you stated. The Minchas Chinuch (Mitzvah 464:41) therefore asks your question on the Rambam: who is going to redeem it if it is going to get burned? He answers that all of Bnei Yisrael will pay to redeem it in order that Hekdesh items should not be burned.

(b) Firstly, everyone punished in a case of Ir ha'Nidachas, besides the missionaries involved in making the people serve Avodah Zarah receives Sayif (sword), not Sekila. Secondly, it is indeed quite a discussion among the Rishonim and Acharonim regarding what exactly happens to the women and children. Many Rishonim, including the Rambam (Hilchos Avodas Kochavim 4:6) and Ramban (Devarim 13:16), seem to hold that even if the women and children themselves did not serve Avodah Zarah they are killed as well. This seems to be a Gezeiras ha'Kasuv (see Minchas Chinuch 464:20). There therefore is no judiciary procedure for the women and children. Once their husband/father is convicted by the Beis Din ha'Gadol (see Rambam ibid.) after it is determined that a majority of the people of the city served Avodah Zarah, they are killed as well.

The reason for this would seem to be akin to Ben Sorer u'Moreh. Nothing good will come of people who were part of a city where the general public was serving Avodah Zarah. Remember, this is at a time when they are fully aware that the Beis Din ha'Gadol might come at any moment and take them and their families to be killed, after they were already warned by Beis Din (see Rambam ibid.). It is possible that the Torah is telling us that people who are so steeped in Avodah Zarah, to the point that they are willing to die for it, affect their wives and children beyond repair.

All the best,

Yaakov Montrose