Arriving at Geneva airport on a Friday evening by Swissair, and then travelling by train to Aigle.
If the plane is late do the railway inspectors get narked and charge you if the train we take is a different one to the booking?
Yes, supersaver tickets are limited to a specific train ride.
From the SBB's terms and conditions:
Supersaver tickets are electronic tickets that can only be used on certain trains and their prices are correspondingly reduced. Supersaver tickets can only be obtained as electronic tickets. Supersaver tickets are personal and are valid only for the day, train (train number) and route printed on the ticket. Booked tickets are not associated with any fixed seat (seat reservation). [...]
Provisions on refunds.
If customers with a supersaver ticket miss their booked connection or want to travel at another time, they can purchase a ticket at the standard tariff and obtain a refund for the supersaver ticket after the journey. To do this, customers must show both their original supersaver ticket with confirmation from the member of the sales or ticket inspection staff and the original ticket at the standard tariff. Only tickets with completely identical routes can be refunded.