That article makes no attempt to explain why Doom isn't a $12M player. It explains why Doom's lack of per-snap production via PFF's ranking system isn't an accurate depiction of what Doom is doing.
His argument is that Doom is a one dimensional speed rusher but that's ok because a one dimensional speed rusher that is good enough at it to demand a double team is still freeing everyone else up. It forces teams into doubling either Doom or Miller while the other is highly likely to beat a one on one match-up.
So the only way Doom isn't worth $12M a year by that article is if you think 3 down speed rush DEs who consistently demand double teams aren't worth $12M, or something close to it.
Where is the 3 down solution to replace Doom in this 9-wide role? Robert Ayers isn't likely to be a wide-9 stud. He's probably better suited to more traditional weakside DE assignments and his best pass rush move is the bull rush, which is far less effective from the wide-9. Do you think he'd even demand a double team if he was suited to the role? Can anyone legitimately argue that Freeney is ever going to demand a double team again?
At that point you're giving up the entire concept of "two guys you have to double team" and instead telling everyone to double Miller and make our opposite side DE combo beat them. A gamble I'm betting most teams will GLADLY take versus a Doom/Miller tandem.