I agree, you would report the NMLS# of the primary MLO as of the date of action taken.
The HMDA Getting it Right guide states:
If more than one individual associated with a Covered Loan or Application meets the definition of “mortgage loan originator,” as defined in Regulation G or Regulation H, a Financial Institution reports the NMLSR ID of the individual mortgage loan originator with primary responsibility for the transaction as of the date of action taken. A Financial Institution that establishes and follows a reasonable, written policy for determining which individual mortgage loan originator has primary responsibility for the reported transaction as of the date of action taken complies with this reporting requirement. Comment 4(a)(34)-3.