From to-morrow's nightly build, version 13.3, there will be a new simuconf.tab option, rural_industries_no_staff_shortage. When this is enabled (which it will be by default, including in older saved games), industries situated outside towns will no longer stop producing/consuming when they are short of staff.
I recommend enabling this at present until a system can be devised to ensure that rural industries are built close enough to towns/villages to allow them to have access to staff in the early years.