Is there any prohibition against paying a small business co-owner as a consultant?

In small business you can hire who you want, just because the employee is also an owner is not prohibited and may be a good idea to have an owner doing the work. If there are other owners they may object according to the governing documents of the business. But on its face this seems fine.
Good Luck

Your question is not entirely clear as to what you are trying to accomplish. There is not some legal prohibition in paying a person as a contractor rather than an employee. While you are free to select the classification, if that classification is incorrect you may be liable for interest, penalties and other costs. The fact that you would like to pay someone as an employee does not alter the requirement that this decision must be consistent with state and federal rules regarding classification.

A series of factors determines whether person should be designated as an employee or as an independent contractor. No one set of factors applies to all situations. For different statutes and circumstances, different tests have been developed to determine how the parties' relationship will be treated. A key element in all of the tests is the right to control the manner and means of the work. If in this relationship the employer has the right to control, the person providing the work is likely an employee and cannot be accurately classified as a contractor. Legally, how the parties themselves label their relationship is not material.

You should really contact a local employment lawyer to discuss your circumstances and how to structure this relationship accurately.

DISCLAIMER—This answer is for informational purposes only and discusses general legal principles, trends, and considerations and is not intended as specific legal advice regarding your question. This answer does not establish an attorney client relationship.