It's been a while, but I believe the Flag in Halo games is technically a weapon just like other guns (someone correct me if I'm wrong). This setup means that to make it throwable, it would need to be made throwable (and figure out how you reconcile what happens to the pistol), which would be just a tad bit dangerous to attempt a weapon tag change like that late in the development process.
On the upside, we know after the Reach TU that 343 doesn't place the same importance on LAN version interoperation like Bungie did, so I'd expect their TUs to make significant changes like that that wouldn't have been possible before with the imposed restrictions.