Now if someone threatens you with adding your site to their disavow list you don't have to worry about your site getting tagged as "spammy". Google has confirmed that having URLS from your website submitted in the disavow file of any backlinks removal company will not have any adverse affect on the page rank of your website.
User Sky T shared an e-mail in the Google Webmaster Help forum that he received from a link removal company. The mail said,
We would like to bring your notice that failure to remove these links would require us to file a "Disavow Links" report with Google. Once we submit these reports to Google they may “flag” your site as "spammy" or otherwise if anything is not in compliance with their guidelines. The last thing we want is to have another webmaster go through this grief.
As a reply, Google's Webmaster Trends Analyst John Mueller commented on the thread, convincing Sky that the comments are entirely wrong. Mueller says that having URLS from your website in the disavow file will cause no harm to your website. According to John,
They are wrong. Having URLs from your website submitted in their disavow file will not cause any problems for your website. One might assume that they are just trying to pressure you. If the comment links they pointed to you are comment spam that was left by them (or by someone working in their name) on your website, perhaps they are willing to help cover the work involved in cleaning their spam up?
Google released the Disavow tool in 2012, so that users can ask Google not to take certain links into account when assessing their site. If you are trying to remove spammy or low quality links from the web and you are unable to advance further, you can disavow the remaining links with the tool. However Google had never specified what it would do to the sites listed in the disavow file. With Mueller's reply to the query, a large part of the confusion seems to be solved now.