Hi Marie...Thanks for sharing your views and guidance.
I agree that disavowing some useful links might push us down in rankings. But I have only disavowed the links which have more Moz spam score after checking them manually. These links look useful and I don't find any value for them. I don't think removing 10 links from our back-link profile with thousands of backlinks will affect us.
I disagree that Google will penalise for using disavow tool. Statement from Matt Cutts is one of the confusing statement to make sure users not misusing the tools and put a load on Google to process the requests. Disavow is complete auto tool with no human interference as per my knowledge and Google will not punish for just using it. And if Google is against experimenting, first they must able to judge if a request is a experiment or genuine try. This is highly impossible for Google which is like trying to read minds of users.
Something interesting happened in our case is....we actually lost the back link from wikipedia page. So we are presuming this might be the obvious cause for the drop. Do you think so?
And do you believe that Google completely ignores bad backlinks? And only good backlinks are ranking factor? (beside on-site factors)