Yes you can disable internally-triggered functions like the activity triggers. The other functions still run, so the timer fires and creates the orchestrator. The orchestrator tries to run the activity functions, but what happens next may not be what you expect.
These are durable functions which are able to keep running. Open the orchestrator function in the Portal and under the Monitor tab you won’t see any errors. There’s an Orchestrations page which will show you what’s happening.
When an activity can’t be called, the orchestration instance stays in the Running state, with the disabled activity in the status Scheduled and the orchestration instance in the status Awaited.
Enable the activity again and the running orchestrations will complete.