Some ideas:

1. Ticket barriers at every station
2. Security guards / police patrols for stations and trains
3. A women-only carriage for late-night services.
4. CCTV on trains that actually works and is monitored.
5. Contracts with TOCs that have clauses about the condition of trains.

I feel very silly for saying this, but maybe we could learn from Thames
Trains by getting security guards to back up Revenue protection staff.
After 10 years the system would pay for itself. 1 staff member could monitor
5 or so DOO trains from a control centre who could be paid lets say £20
grand a year. On trains with other staff they can monitor the train
themselves. They can then contact the driver of the train or the
BTP/Security staff who can deal with the matter.