The only danger is if you disavow the wrong links. As long as you are careful not to include legitimate links in with the bad ones in the disavow file you should be fine.
Best practices involve doing a link audit and sorting things out, then contacting webmasters about taking down the links, then running the disavow. Given the apparent clarity that this was an external negative SEO campaign I would consider skipping the second step and including a comment regarding your theory on the origination of the links in the disavow file... but I've never tried that. I've only been in situations where the disavow was based on misguided previous seo efforts, so we went through the removal step.
Hopefully someone else can jump in on that.
