I am a non resident(five years on F1 completes in 2012) but will be filing 2008 taxes jointly with spouse who is a resident. As I found out I will need to start paying FICA taxes for 2009. However, my college payroll will not be deducting them from my salary since in their system I am non-resident until 2012. What should I do? Should I pay them with the 2009 return next year and will I be penalized for underpayment? Is there a way to keep paying in 2008?

You can not file 2008 tax return as resident. On F1/OPT you are exempt from residency for 5-years. You must file non-resident tax return and Form 8843. Your income is not subject to FICA taxes.
Read: Your U.S. Tax Return: U.S. Tax Filing Requirements for Non-Residents