There is nothing wrong, as far as Islam is concerned, in holding the marriage ceremony in a Church as long as the conditions of Islamic marriage are met and one avoids participating in the Church rites.
It is a well-known fact that Muslim men are allowed to marry non-Muslim women from among Ahl Al-Kitab or the People of the Book. Allah Almighty says, (This day are (all) good things made lawful for you. The food of those who have received the Scripture is lawful for you, and your food is lawful for them. And so are the virtuous women of the believers and the virtuous women of those who received the Scripture before you (lawful for you) when ye give them their marriage portions and live with them in honour, not in fornication, nor taking them as secret concubines…) (Al-Ma’idah: 5)
At the same time, we must realize that the scholars have put stipulations and conditions to this proposed marriage. The main ones are as follows:
1. That it occurs in a Muslim country.
2. That there is no fear that the children, or the husband, will be negatively affected by the non-Muslim wife and or mother.
Regarding the question if it is permissible to hold wedding ceremonies in a Church, for example if the wife-to-be stipulated doing so, then there is nothing wrong in that, as long as the marriage conditions and prerequisites are fulfilled according to the Islamic Shari`ah. We have to keep in mind that such conditions have to be met before going to the Church.
On the other hand, if it is not necessary to go to the Church, then there is no need to hold any ceremonies there.