In theory, splitting up the farm bill to deal separately with farm policy and nutrition assistance makes a lot of sense.
Farm subsidies used to go mostly to actual farmers who could use the help. So while the pairing of farm aid and food aid was always politically motivated, it also made some sense: the farm bill was safety-net legislation, and food stamps fit right into that. As agriculture has changed, agricultural policy has become more and more of a mess of corporate welfare that's against the public interest. And one big thing protecting this status quo has been the fact that liberals can't vote against a business-as-usual farm bill, because it's also how hungry people get fed.