how would you leave a faction?

Is there a command or am I suppose to write a note?

No. To avoid faction / clan hopping, you need either to ask their leader (mort or Imm) to remove you or ask an E / L of the new faction / clan to draft you.

I tried to draft someone as an E recently.  The message I got in game said they have to leave their previous clan first.

I've had an E try on me previously and I've tried as an L.  If you're a member of the Academy, you have to go through the respective clan guard.  Any other feeder clan I believe you need an Imm to do it.