Can you add more SLA rules so that the SLA 'counter' is only running when the ticket is waiting on agents, i.e. the ticket status is Open or Pending. When the ticket status is any other status, it doesn't count towards the SLA.
For example, if a ticket which has a resolution SLA of 1 hour and the agent responds within 10 minutes of the ticket being opened with a question back to the customer, the status is then set to waiting on customer. Until the customer replies, the sla time elapsed will only ever be 10 minutes. Once the customer replies, the ticket goes to open automatically, and the timer starts again.
There is an SLA timer slider (on/off) next to most every ticket status. This determines if the SLA timer is ticking for a ticket in each specific status. It works in conjunction with your applicable SLA policy. OPEN will always tick for both SLA response and resolution, while Resolved and Closed will never tick for either.
If you want the time the agent is waiting on a response to NOT count, you would need to create a status (e.g., Waiting on Customer) and turn the SLA timer slider OFF. The agent would need to change the status of the ticket to this when responding to the customer. This is what we do.