If we could "cure" some of the sicknesses/deficits/mental illnesses/etc that make people more likely to be fundies, that would certainly be super. That could conceivably be done on an individual level, but would also need to be done on a societal level. It wouldn't necessarily be targeting religion. Reducing psychosis, paranoia and extreme obsessiveness, for example, could conceivably reduce religiosity- but would, of course, be fought by the systems outside the individual. In general, finding ways to reduce psychosis/paranoia/obsessiveness/etc are certainly worthwhile goals, and we're still not all that great at any of them, quite frankly.
Religion often provides people with a support system, and often provides them with a sense of hope. Ripping that away without giving something else to replace it would, in some cases, be needlessly devastating.