Well, this absolutely sucks.
From what you say though, I suspect you got an Acas adviser who thought the same, but actually doesn't know how to help you and hopes appealing to their better nature would work.
The trouble is that there are very strict rules around calculating SMP and the employer doesn't have wriggle room to use any discretion. It's always been the case for example that women are warned about salary sacrifice schemes in the crucial week 18-25 period in case it affects the calculation.
In this case it seems particularly unfair because if they had paid you correctly the first time you would have been paid properly during this period!
Two options
a) a formal grievance setting out why you believe they should pay you an additional amount to top you up to what your correct SMP should have been. Are we talking aboit the first 6 weeks at 90% calculation here? If you can show them the amount it might be less than they fear.
b) having done that, if they don't agree, go to the HMRC statutory pay disputes team and ask them to determine it.
I am not so sure about the chances of a discrimination claim tbh. Just thinking it through and you would need a comparator for a sex discrimination claim. A man would not be claiming entitlement to SMP so that falls away. For pregnancy and maternity discrimination you don't need a comparator but you do need to show you were treated unfavourably because of your pregnancy. I am not sure how you would show that here. They are reclaiming an overpayment and applying the law on SMP calculations, both of which they are entitled (and correct!) To do. Unless you could perhaps say they don't normally recoup overpayments generally and this was therefore aimed at you? But the reason for the reduced SMP isn't their decision but the legal calculation. (And it sounds as though the repayment schedule started before they knew you were pregnant?).