I understand what you mean. I think that the reason Pandoc has disallowed putting periods at the end of citekeys is that it truly does not represent a behavior that any users engage in, and disallowing it massively simplifies the Markdown or org syntax of a very common procedure: putting a period at the end of a list of citations in a footnote. In any case, I can understand hesitance to break from strict bibtex specifications.
Currently, a zero-width space does not properly escape a period, either. It has the same effect as a regular space (see first email). One gets a citation followed by “,.” or “, .” The broader problem is that org-export currently assumes that any text following a citation must be exported with a comma and a space following the citation, e.g. “Jones 2013, lorem ipsum.” Perhaps we could solve both problems at once by introducing an escape sequence that signals Org not to apply that default behavior. A zero-width space is fine by me, if it would activate that behavior, though I think that a human-readable escape character would be preferable here. I should mention that "\-“ would not be ideal, as a writer may like to follow a footnoted citation with an em-dash ("---“).