Sounds like you're going to be doing a lot of writes, which neo4j isn't designed for. While I get why you're using it, I'd suggest that it's not really the right tool for that job, which is possibly why you're having problems with it.

Do you really need persistance at all? If the application crashes everyone would be kicked out of the channels anyway no? I think making an in memory graph and ditching the graph DB entirely would be more helpful for that kind of suggestion tool.