I'm now in a position to answer my own question with a reasonable degree of confidence. The short answer is "no".
A council must, by statute, record its decisions in minutes. There is no statutory basis for there being more than one set of minutes, and legal opinion is that having more than one set of minutes is not advisable. In any case, it appears that the Local Government Act 1972 section 228 gives electors an absolute right to inspect signed minutes. There is also a statutory requirement that minutes be signed promptly (normally at the same or the next meeting and certainly not deliberately delayed).
The Freedom of Information Act is not relevant, because the right to inspect minutes is a specific statutory right. The Data Protection Act is also not relevant, because it does not override a specific obligation to provide information (as in section 228). Allowing inspection of a minute cannot, therefore, be a breach of the DPA.
Clearly in delicate situations it is advisble to be circumspect about what is recorded in minutes. At any time, only the decisions need to be recorded, and not the discussion or any ancillary papers (which may be subject to FoI but could be exempted).
So it seems that there is no lawful route to keeping a minute confidential beyond the period between its recording and its signing, which cannot be delayed for long.
The information above is based on the statutes, the general advice issued by the National Association of Local Councils and advice given by a solicitor specialising in local council law.