I imagine that unscrupulous individuals or organisations may try paying for votes, to sway a referendum. Both buying and selling votes would be illegal and it would be the role of the police to identify and prosecute those involved. As perpetrators of large scale vote buying would need to advertise in some way (if only by word of mouth) then they should be easy to identify.
Additional technological ways of identifying fraudsters may also be employed. Detecting patterns of access by servers may identify fraudsters: vote buyers would need to verify that vote sellers had cast the votes they paid for, creating blips in on-line activity after the referendum.
Also, requiring a significant majority to win means that rigging a vote requires a "big crime", which is more easily detected.