The states that were in rebellion could call themselves anything they wanted -- they were not, to my knowledge, recognized as a sovereign nation by any nation anywhere in the world. The US did not recognize their right to secede and always considered them part of the Union. Therefore their flags are HISTORIC flags, much as the flag (if any) of the State of Franklin would be historic (as is the Franklin story itself).

What is past is past -- honor the valor, hate the stupidity, and be disgusted with attempts to use history to provoke division once again.