So there seem to be a few issues combining here.
1: A provisional deal has been done; though it may be DCO with a guaranteed OBS on every service rather than Guards closing doors. This will cost more than the planned DOO, with OBS on selected services. Therefore Merseyrail need to find more money.
2: Ways of saving or raising money; Closing or reducing hours at ticket offices (possibly redeploying staff as OBSs), ticket machines that accept cards, e-ticketing, fare rises, pay freezes, reducing fare evasion. These are either things which should be done already or potentially controversial.
3: The level of subsidy on Merseyrail; It's likely quite high, but the problem with raising fares is that driving, cycling, bus are all valid alternatives for commuters who actually pay for peak returns/season tickets and not the cheap off-peak tickets. Therefore, if prices go up too much the number of passengers is likely to go down. This is probably made worse by the fact that pensioner's travelcards are valid on Merseyrail, therefore 'fare revenue' may involve an amount from the councils.
4: New v Refurbished stock; Merseyrail have used the 507/8s for 40 years, provided the new trains are designed and used for a similar length of time I'm not entirely convinced refurbishing trains from elsewhere would be much cheaper over the full period. Also, it would be difficult to get the level platform access in anything but custom builds.