If you’re on the Safe Browsing list, people will probably have some issues connecting to you normally. It’s currently one of the best sources for sites that have been flagged as harmful. If your site is on it, it’s not too painful to fix the issue and get removed before getting that certificate issued. A lot of other issuers will also use the same or a similar resource.
If the list becomes unreliable, LE could switch sources. Maybe they could use the source for McAfee SiteAdvisor, or Yandex’s list then.