My worry is that whether retroactive changes to a fully executed employment agreement at this point would pass muster and substituting the reimbursement for other types of payment now could be taken as form over substance.

Any change should be considered in conjunction with §4980D(c) which provides that the excise tax may not apply so long as certain conditions are met and that the correction is made within a narrow window.  This must also overcome the hurdle of reasonable cause and willful neglect which could prove challenging.