People openly talk about this as the reason that HackerNews continues to be such a vibrant community.
Replacing the mods will change the community, full stop. Could be for the better , could be for the worse.
Conversely, the mods can also be mercurial and act like little tyrants over the subreddit. /r/StarTrek in particular is known for stifling criticism around 'new trek' and spinoff subreddits like /r/DaystromInstitute were created by people tired of the mods' actions.
It also raises an interesting question as to why the mods have so much power in the first place and if any community recourse should exist when subscribers do not like the mods' actions. For one thing it does seem weird that the mods of r/StarTrek are allowed to unilaterally close the subreddit.
I also don't think mods should be able to turn /r subs private. The private subs should be on a different path like /p. If you turn a /r sub private then it converts to /p and the /r subname becomes available again.
I suspect that some reform around private subs will be instituted in the near-ish future since it is the primary tool used by mods in the boycott.