Making best use of existing capacity is important - and managing this whilst all the work is going on will be key.
Off peak discounted rates already apply and are used by some carriers to operate routes where the timings are not too critical and an away based aircraft can be utilized.
I'm sure that most of the big carriers will understand that things will be difficult during the transformation, but provided they can see the end benefits, they will be prepared to put up with some inconvenience. This could be seen prior to the R2 opening, when they were prepared to accept greater than normal ATC delays as they saw the benefits to come.
Hopefully the Airport are keeping the users regularly up to date with developments in the programme, are listening to their concerns and trying to accommodate them where they can or explaining to customers why certain thing's can't be done. That way everyone feels involved.