The Little Sisters refused to sign a form saying they opposed birth control because another entity, using other funds, would provide the ability of their employees to obtain BC.  This was cooperation with evil. But, the Little Sisters continue to provide their employees wages.  Those directly paid wages provide their employees the ability to buy BC.  It is those directly paid wages that are now used to do that, not monies from some other entity.  In addition, the wages paid their employees are taxed and are used to issue marriage licenses to SS couples, provide funding to Planned Parenthood, execute prisoners, provide BC to other individuals under Obamacare,  etc.   The Government's response to their initial objection was reasonable.