Yes all battery chargers (including 36 Volt chargers) can be connected directly to the battery pack without going through the controller.
Inside of all electric scooter and bike speed controllers which I have seen the battery charger port connector wires are attached directly to the battery pack connector wires, so the charger is wired directly to the batteries when it goes through the controller.
Please let us know if you have any further questions.
Luca B