Married filing separately and wife contributed to Roth IRA

Married filing separately since 2012 in order to reduce the amount I pay for Income Based Fed Loans. Wife contributed to Roth in 2012 to 2016. She made over the $10,000 limit. What should we do? Can I transfer the $12,000 to a traditional to avoid further penalty? Can you explain my penalties? Is it 6% per year until the money is removed from the Roth? So do I owe $144 in 2012, $288 for 2013, $432 for 2014, $576 for 2015? Hopefully can transfer the $2400 to traditional before the 18th to avoid penalty this year.