[PvK]

Oh, in SEIV? I thought you meant with real-world computers, at first.

Aside from avoiding getting hit, or killing the attacker first, or not having any master computers, the only defense is to add bridge/life support/crew quarters to the ship, so if the master computer dies, there is no adverse effect (except the loss of 10 structure points).

For example, a dreadnought with a master computer can have a bridge and just one life support and crew quarters component. It is then effectively immune to computer virus and allegiance subverter, and has a little more space available than a ship without an MC, although it will cost a bit more. In the unmodded game, that is.

PvK