I notice that you said the Clerk decided to give a dispensation. The Clerk has no powers to do this. The dispensation must be debated and approved, in public, by the body to which it applies, i.e. full council, committee, sub-committee etc and the reasons for the dispensation must be recorded in the minutes. As somebodyelse has stated, the normal reason for doing this is to prevent a meeting from becoming inquorate on a particular matter. This is increasingly common in small parishes for agenda items relating to village halls, where the same few people might serve as parish councillors and village hall trustees. Inquoracy appears not to be the issue in your case.
A CIC is a commercial company and, as such, may pay its directors a salary and/or a share of profits. This is the main reason a CIC cannot be granted charitable status or any of the tax benefits offered to charitable organisations. Unless the governing document of your CIC specifically excludes this provision, I believe the directors should declare a pecuniary interest and withdraw from the meeting whilst the CIC is under discussion.
On a wider issue, as someone who used to cycle through your village, I think it would be a challenge to establish a viable village shop business there, due to the size, geography and the absence of passing trade and, as the village appears to be split over the issue, I fear it is doomed to fail. I have recently been involved in a similar project in a slightly larger and more tightly defined but equally isolated village. Sadly, it was not sustainable.