I think Carol’s solution is the most obvious one. The fact that DWP has awarded SC to one of them on the basis that s/he has a partner does not prevent you from treating them as single people if you think you know better; although the AIF restricts your room for manoeuvre in the means-test arithmetic for the one who is the DWP’s claimant (basically you’ll be stuck with a single applicable amount and a couple’s AIF).
If you were to aggregate them as a couple, you would not be able to award CTB separately to each of them because s134 of the Contributions and Benefits Act prevents different members of the same family from getting the same means-tested benefit (a necessary provision to prevent duplication, but a snag in this particular case). So if you go down the couple route you would have to look at awarding two lots of CTB to the same claimant. This rapidly unravels in confusion: both members of a couple should be jointly liable for CT, so there is no need for a deeming rule in CTB akin to HB Reg 8 (partner of liable person treated as liable for rent); but for billing purposes your authority presumably does not regard these two as jointly liable members of a couple because each has been deemed resident in their own dwelling. I am not sure where that leaves a CTB claim on behalf of the couple – it should be impossible to achieve this situation and so the legislation doesn’t cater for it in the same way that HB Reg 7(6) does for rent.
Therefore the only workable way forward seems to be to regard the SC position as an anomaly and assess CTB in the same way you have determined liability: allow each of them to claim CTB as a single person, with a slightly unfair means test for one of them unless and until the DWP changes its mind about the SC aggregation.