@jimbeetle, thanks a lot.
I would still personally disavow those links too, just in case.
@Planet13, yeah, I know what you mean. It's just there's always that little bit of fear when using the disavow tool. It's like saying "sorry, Google, I've done something wrong" when in fact you haven't...
@JS_Harris, the funny thing is that the site is neither penalised nor affected by any algo update. It ranks where it is supposed to rank considering its legitimate backlink profile.
That, however, is not a good enough measurement. I still see several extremely spammy sites ranking well even after the recent Penguin. Even if this site was not penalised in May, it might get wiped out in the future (if those toxic links are still considered by Google).
I've spoken to many webmasters who've used the disavow tool and just like JS_Harris, they've never seen any tangible results. I bet the conspiracy theorists rejoice because some think that the whole disavow tool is a phishing tactic by Google. I personally wouldn't go that far. Maybe it's a good tool for them to learn more about spam?
Anyway, I feel a little bit apprehensive putting a totally white-hat site on Google's radar... but I also feel tempted to do it just to be on the safe side... decisions, decisions!