Hi
I know that there was an Independent Chapel in Wilton around the time you are interested in. I think it was later a Presbyterian one. There was also a Methodist Chapel there.
Until around 5 years ago there was a joint United Reformed (which is a later amalgamation of the Presbyterians and Congregationalists) and Methodist Church who met in St Edith's in Wilton. This building was also used by the Roman Catholics in Wilton. I think that before the free Churches met in St Edith's the chapel was in Crow Lane, Wilton. However, the building was in quite a bad state of repair and the Church closed and the remaining members went to worship elsewhere (I don't think there were very many by this time). Before the Church closed down the URC/Methodist part was part of a joint pastorate with the URC Church in Salisbury and had the same Minister. I am a member of the Salisbury Church and have just done an extensive hidtory of the Church and been through all the records held both in Chippenham Records Office and the few bits that were still in the Church. However, there was no records among them pertaining to Wilton. However, there may well be records of the Wilton Church held seperately at Chppenham. I would have thought it was worth a look. Have you tried searching the A2A site, which you can now access through the National Archives website? You could also try some of the Anglican churches on the edge of Wilton, for example the one at Fugglestone (St Peter's??). There may be records held by the Methodist Circuit too.
Hope this helps point you in the right direction!
Fiona