There cannot be a cover up when the process is being overseen by WADA. This is not something the AFL have any control over. Initially they were able to control the message getting out whilst assisting the ASADA investigation. Since the AFL's involvement in the investigation was completed in August 2013, ASADA have interviewed a number of key witnesses & the AFL is not privy to the content of these interviews.
You will find that much of what was established post August 2013 has played a part in Dank getting his show cause notice & the ADRVP being convened to make a determination on the evidence before them. Should the ADRVP determine Dank should receive an infraction, it will be up to the relevant authority, in this case the AFL, to determine a penalty (if the AFL try to fudge this, WADA will appeal & then the fun really starts). If Dank is infracted, this will start the dominoes falling. Remember Dank was an employee of the EFC, therefore any guilt attached to him also belongs to the EFC. The AFL will have no choice but to penalise the club, & some individuals, under its anti-doping rules. How far this reaches remains to be seen however any watering down of penalties, or attempted cover-ups by the AFL will be pounced on by WADA & it won't be pretty for the AFL.
Ask yourself why is Demetriou prepared to step down this year, when he knows he can stay on as long as he wants, with the full support of the AFL Commission. The answer is most likely that the taint which is going to come from the fallout of the ASADA investigation would make Demetriou's position untenable. By announcing his intention to stand down before the proverbial shit hits the fan, he can have the next stage of his career sorted without the stench from the Essendope doping debacle following him, particularly if the AFL, under his leadership, has appropriately punished those found guilty of breaching the code's anti-doping laws.