Flag Ceremonies are offered universally. Whether someone may have an irrational hatred of CFA does not convert a flag ceremony or Pledge of Allegiance into an endorsement of CFA, any more than a flag ceremony at a Republican, Democrat, Libertarian, or Green Party political rally does. Because it is a display of loyalty to the nation, the ceremony is ALWAYS acceptable and deemed to be part of the civic process.
The Troop Committee's role is to advise the Scoutmaster on BSA policies. If they can't point to a BSA policy that prohibits the Scouts from this sort of activity, they should be told, in a courteous and kind manner, to back off. In this case, BSA's policy expressly allows the scouts to perform this sort of civic duty for businesses, churches, and political events. Planned Parenthood? Sure. CFA? Sure.
If you don't want to count them as service hours, that's fine. Service to me means something out-of-the-ordinary, something the Scouts go out of their way to do. Maybe something they wouldn't typically do over the course of their day. But Flag ceremonies? That's kind of something Scouts do.