Yes, at that time there were no clear instructions available. Having checked in the evening before resulted being on the preliminary passenger manifest and that was enough for CPB to cancel the ESTA. Apart from that I can confirm that documentation will be checked during check-in at the airport (in my case it was in Frankfurt) by the airline's embassy / CPB liaison.
Maybe worth mentioning as well: During a subsequent trip with the CR-1 visa in my passport they still had to check my marriage cert, the visa itself was not sufficient even though it stated that I was exempt from the proclamations...
JJ-RS got a reaction from Chancy in Immediate relative entering on VWP/ESTA