Hi,
I think the registering part needs to be done at application start. But you can try if it works on runtime using the sample on devnet:
https://docs.kentico.com/display/K82/Creating+integration+connectors
If it doesn't work and the its per site you could let your custom module enable/disable the connector object itself. Or you could do a check in code of the task to see if a custom setting (you created and can update in your module) is enabled.
Greets,
David