They can be reimbursed for the cost of health insurance.  The cost of the health insurance is the full amount, and the full amount is what should have been reimbursed the entire time.  What personal credit that taxpayer qualifies for should not affect the amount of the reimbursement.

As for your actual question for what to do now, yes, it can be reimbursed, but the real question is if the reimbursement will be subject to FICA or not.

Although my personal opinion is that logically it should follow the rules of a Accountable Plan (which requires timely reimbursement), I'm not aware of anything that actually states that.  In fact, Notice 2008-1 says "the S corporation reimburses the 2-percent shareholder-employee for the premium payments in the current taxable year", which seems to say it can be done anytime.