Does Northern Cavalry Flank kneel when attacking someone with a character agenda or does the character agenda not count as an agenda for cards like NCF?

If the character agenda is active (i.e. the character has died and is now attached to the house card as the only agenda), then they are running an agenda. It doesn't matter if it's a regular agenda or character-turned-agenda.

In this example, no, NCF will not kneel to attack that person.

Point of interest. NCF will not kneel to attack any player if even 1 player has an agenda, the wording of the text does not stipulate that they will not kneel to attack the player with the agenda, just that they do not kneel.