If you want to go down that path your could force them to buy a V/Line paper ticket which could cost the Metro fare plus $10 or something like that.Bendigo and Traralgon services are both fully myki apply and both Sunbury and Pakenham users pay same amount of fare as person wishing to travel from Melbourne to any of these locations: Riddlers Creek, Wandong and Bacchus Marsh.
The only problem of Sunbury and Pakenham using the V/Line is peak pm time(services from Melbourne) and then you can't tell the difference between a person get off at Metro station or person get off a V/Line station because everyone has a myki with them.
The best solution is run a train service that does the following:
Long term future ( which I think should happen:
1st tier: Watergarden (every 2nd train from Sunbury) to Dandenong via the Melbourne metro tunnel (run as 10mins metro train style service)
2nd tier: Bendigo stopping all stations to Watergarden and then limited stops via Flinders Street to Dandenong and then stopping all stations to Traralgon