The boy was definitely Kelmomas, and the "woman" was a skin-spy taking Esmenet's form, yes.
I don't think the Consult sent that skin-spy after Kelmomas specifically. There were probably skin-spies around, since Cnaiür had tricked the Serwë skin-spy into thinking the Scylvendi would fight for their side. That one probably decided to take Kelmomas to the Ark because of the prophecy mentioned in TWLW by Aurang and Tsuör (the skin-spy impersonating Soma).