I paid back tuition reimbursement to my employer when I left but the amount is still reflected as income in my W2, how do I reflect that my income was actually less?

The best way would be to request a corrected W-2 from your employer who would have to give you a new W-@ and supply the copy to the IRS.  It will take time now but may keep the IRS from taking a close look at your return.

The company sends a W-2 to the IRS and what you enter should match what they send. 

 You could subtract the amount from the W-2 and wait for the IRS to ask you the reason for the discrepancy from what the employer sent.  That is when you would supply the documents to support why you changed the total.