I spoke to Customer Service, and a very helpful gentleman there.

Basically if I phone prior to 3 hours to change the flight back by a day (before 2pm Malta time) it will cost me 629 TND - about 200 euros.
If I phone within 3 hours, even if checked in it'll be classed as a no show, and flights fully cancelled. That'll cost me (or travel insurance company) about 13,600 TND for a new ticket - 4,200 euros for the 2 of us travelling.

So here's my plan:
1. Check in online 48 hours before. That means they're expecting us at the gate. Not sure what time they'll close the gate (30 mins prior to take off?)
1. Monitor the incoming flight (https://www.flightradar24.com/data/flights/ug1300) and see if its arriving on time. If its not left by noon Malta time, phone Qatar and pay the 629 TND change fee. That way we relax and just wait for the flight to arrive at whatever time.
2. If the flight is on time, don't call Qatar, but risk it gets to TUN in time.
4. Make the flight If we don't make it all the way to the gate in time before its closed, then we call Qatar and get booked onto the flight the next day - 13,600 TND and claim on travel insurance.

Fingers crossed!