I think its almost a given that fares via HS2 will be higher than current WCML fares despite what the current government says, it does not tie the hands of the next. services on classic lines in Kent to London were slowed down, and this is from those that used them, to make HS1 services more attractive and it also has HS1 specific fares. The same will happen for HS2.
I still think you will have some catering between Birmingham and London and Crewe to London via WCML as not all the intermediate stations will be 'served' by HS2 but will still be long journeys. The same on the MML and ECML.
What will see the end of it will be station catering and prices of catering on trains relative to off train catering. If trains price themselves too high relative to the competition then there will be fewer sales and hence closure.
Let's look at some numbers:
A 390 has 470 seats/589 seats Vs ~1,100 seats on a HS2 train. Given that you need one just one driver regardless as to which train they are driving. That means that the cost of the driver on the HS2 train costs less per seat.
Next up, there's either 9 or 11 coaches on each train on the 390's over the (say) 16 coaches on a 400m long HS2. Does that mean that the leading costs will be higher? Well possibly not and here's why.
The current services to Manchester takes 2 hours, so a round trip for each unit of 5 hours. HS2 this drops to 3 hours. At 9 coaches over 5 hours for 3 services that requires 135 coaches (which is the very minimum of coaches, this rises to 165 coaches). This compares with 144 coaches for HS2.
Therefore, given that some services are going to be 11 coaches currently, the last costs are likely to be similar, even though there'll be a lot more seats.
This time saving also reduces the number of staff required to run the same number of services. This further reducing the cost per seat.
Therefore if you earn as much money in total as you did before then you're going to be making more money.
Given that Virgin had been paying a premium to the DfT then this money (as well as the extra profits from the lower costs) would be able to pay for the relevant costs of building the line in the first place (I say relevant costs as some of the costs are paid back through taxes).