Once upon a time when I had an itty bitty pack - I disconnected the controller. Always hated hooking it back up. ZAP! Scare the piss outta me. But that woz a long time ago
Today I leave my controllers connected.
Sometimes I will use the charger alone without the batteries to debug a problem, but that is very rare.
It is also rare to charge and have the controllers "on"; I might be checking a stat on the CA, or maybe messing with the lights during the interval - but that's it.
Most of the time the controllers are off, and the lil' lipos are happy as Larry charging away.
Charging away, KF