I could see the case for a penalty if a player for Team Darkness with a mark subbed me and used the mark, but that didn't happen.
If I had let someone from Team Darkness without a darkness mark sub me and replace the mark with a pillar, this match would have had no penalty at all.
But because I didn't unnecessarily delay, I apparently ought to be penalized.
Also to those worried about this setting a precedent, allowing people to downgrade from a mark card to a pillar anytime seems alright to me.
Rules regarding substitution are irrelevant here - the issue is that you fielded a deck containing cards you do not have access to.
No penalty will be applied in this case, however, let this serve as a warning that penalties may be given in future rounds for players submitting decks to their vault which they cannot field. The rules will be updated to reflect this.