Is the pending refund an individual or a joint refund? Is it being direct deposited or is someone getting a check?
If it is individual, then it's a no brainer, it is yours. If it's joint... you are going to need to divy up that money.
I think the "fair" thing to do would be for both parties to input their information into a free online service (like TurboTax or TaxCut) and see how much they would get as a refund if they filed individually. Say the refund is $4,000. Harry puts in his info and he would have gotten back $3,000 filing individual. Sally puts her info in and she would have gotten $500. There is a difference of $500. So, split it. Harry gets $3,250 and Sally gets $750. No harm, no foul.
Once all the dividing is agreed upon, you may want to look into having both parties sign a statement about how all this went down, just to CYA.
especially important
the IRS may come back a few years down the road and say you didn't file something correctly and you have to correct it now. If you have this statement, then you can tell exactly what happened and go from there. For example, Sally couldn't later say, "but Harry, you kept the whole refund!"