My answer would be yes, as long as it was rolled during an official league and you do pay for your sanction in a timely manner it will count. You should check with the President or VP of your league though as it is up to them to enter your honor score(s) with the USBC.

My league isn't paying for sanction until at least week 2 because the USBC is late getting the cards to the league.  I'm sure this won't impact any scores rolled during the first two weeks.