At Manifest 1.0, several people threatened to not attend if Richard Hanania was allowed to attend and/or speak. Manifold ended up prohibiting him from being a speaker, but allowing him to attend.
(Further background and discussion here, here, here, and here.)
"Due to threats" refers to Manifold making the decision not out of their own personal preferences, but because attendees threatened to not come or to do something else that Manifold finds detrimental. This includes justifications along the lines of "more people dislike X than like X, so it's utility-maximizing to ban them". It also includes situations where the threats were implied, such as lots of people aggressivly telling Manifold how uncomfortable they would be if X were to attend, without explicitly threatening any action.
If Manifold doesn't make their decision process public, I'll take my best guess. I won't bet.