The "stick" idea won't work, because the targets are people who don't have anything to lose. Any benefits you grab to pay for these penalties will likely be limited to food stamps and rent help, i.e. the very things keeping their kids fed and housed so they have a remote chance of succeeding in school.
A better approach is to use the "carrot" of conditional cash transfers (CCTs). These programs have been proven to work well in impoverished third world environments and a pilot program in NYC saw some success.
http://en.wikipedia.org/wiki/Conditional_cash_transfer Basically, you give money to the parents for keeping their kids vaccinated, getting regular checkups, and for school attendance. It's not a panacea but if appropriately targeted at very poor communities, could make an impact in breaking the poverty cycle.