As i presume that you are giving discounts based on the payment term as a Condition...
"""We have 2 Sold-Tos with the same Payer. The Payer gets a discount with will apply to both Sold-tos since the payment terms are getting pulled from the Payer. When sales order is created, payment terms get pulled from Payer and both Sold-Tos gets a discount. But we only want to offer discount to only one of the Sold-Tos but the other sold to doesn't get a discount.""""
Have you tried by Keeping Sold to party as a condition in your pricing table and assign this your Discount condition type???(KUNAG--Sold to party)
Otherwise as suggested by Our Legend-- you can try with Enhancement in MV45AFZZ...
Phanikumar