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. (Not, at least not terribly much, by the churches.)
In order for a more common-sense approach to farm policy and food stamps to actually be helpful, we also need a common-sense conversation about food stamps themselves. Unfortunately, that's not the conversation we have. Food stamps recipients are too often dismissed as "takers" or even villified as "moochers." In reality, food stamps go mostly to working families, disproportionately—"welfare queen" dog whistlers beware—rural ones (pdf). Food stamps keep these families out of poverty. And they help the economy, a lot.
Yes, food stamps cost money. And as long as gutting safety-net spending is the dominant theme in the House of Representatives, programs like food stamps will be at risk regardless of how much good they do or how efficiently. Until that changes, a convoluted farm bill that preserves food stamps (or rather, only cuts them a little) remains the least of several evils.