Sorry for finding this question rather late; if you've not yet found out (or anybody else new to this wants to know), I'll tell you:

1) As soon as you can enter the "cyberspace", you should also be able to switch to "augmented reality" ("AR"). In this mode, put the cross onto the gun, movement of real-lfe objects and persons will be "frozen", but you must avoid viruses floating around. On the gun, press "ENTER" on the keyboard, until the gun gets deactivated, however, as soon as you press the button, the viruses will come after you.

2) I could not test this due to a bug, but you should also be able to shoot back at them, if you've got a gun.

3) Sometimes you can avoid them.