There's a new setting called 'random-rainbows-minimum-online-players'. This allows you to specify the amount of online players that are needed to start the random rainbow event. It's set to 0 by default. When set to 0, the random rainbows will always spawn, no matter the online player-count. If the required player-count isn't met, the plugin will skip that random rainbow spawn, once more players log in it will just continue as usual.
Note:
Make sure you regenerate the new config setting, or manually add it to your config file if you want to use this feature.