Is working for a company that produces non-alcoholic beverages, but has another division that produces alcoholic drinks, permissible due to the commingled capital?

If the department is completely independent of alcohol production, and its production line is not used for that purpose, then working in it is permissible, even if there are other departments in the same company that work with alcohol. The mixing of the company's money does not cause harm, because if lawful money mixes with unlawful money, the lawful money does not become unlawful.