I'm going to make a gross assumption here, but please play along.
Between the blog network de-indexation and the Penguin update it's hard to deny that at least there is a real possibility that links can harm a site. That's the assumption. These could be from Negative SEO, bad prior habits, or any brand of potential harmful scheme. The source doesn't matter for this debate.
The question I'd like to open is: Should webmasters spend time working to remove bad links? Should they be aware of "unauthorized" links and actively work to remove them? Should they police their own link profile to prevent overuse of keyword anchors? If they should, what is the time split.
Fifth - If you live in an apartment block, and one of your neighbors opens a crack den, or something that the cops won't like, or does something the city thinks is dangerous, they may seal off the entry to all of your visitors too..
referring to my recent experience ( reported here ) of having a small group of domains de-indexed by Google, because of what someone else did on their domain on the shared IP I had left those domains on for years..I moved mine to my their own dedi IPs within a few hours of finding that the shared IP was de-indexed..
Instant recovery of all rankings ..:)
The rest of my old co-tenants are still "walled" off , and can't be found..