There were also underlying security issues. Most of the messaging apps Tor Messenger supported are based on client-server architectures, and those can leak metadata (such as who's involved in a conversation and when) that might reveal who your friends are. There was no real way for the Tor crew to mitigate these issues.

There aren't many viable alternatives. Tor suggests CoyIM, but it's prone to the same metadata issues as Messenger. You may have to accept that a small amount of chat data could find its way into the wrong hands, even if the actual conversations are locked down tight.