If the ferries are attracting lots of cyclists, shouldn't that be seen as an opportunity for CalMac, rather than a problem?
Drivers/passengers are charged separately to vehicles so ignore the cost of the passengers - it is the same price that a cyclist pays, £6.90 return.
What about the cost of the vehicle? A return trip to Mull from Oban is £26 for a car. CalMac could come up with some kind of bike storage rack which could be folded down to take the place of a car. I'm fairly sure that you could get 10 bikes in the space needed for one car if the racks were designed sensibly.
In that case if cyclists in a group were each prepared to pay (say) £3 for a return trip for the bike on top of their £6.90 then CalMac could charge £30 for 10 bikes instead of £26 for one car. They could still have (say) 6 free bike places. Any bikes beyond those 6 would have to go in one of the racks and the charge would be £3 return. 3 adults sharing the cost of going by car would pay £15.57 each return. Cyclists paying the bike charge would pay £9.90 return. Ok, it would be a big price hike on £6.90, but it would still be a good deal, and that extra charge could be avoided by reserving one of the free bike places. If the racks could fit more than 10 bikes per car space then the bike charge could be reduced.