Origins PvE server. A friend spawned on the bridge where we logged out last night. As he crossed to the bigger island - he was shot. As it's a PvE server - can this only be an NPC who killed him?

depends on what bridge it was

I think it's the upper bridge from small Island to bigger island. The northern bridge - if that helps

Added in 1 minute 45 seconds:
Chernovar /Veditch area

there could be the mission "ambush" near the toll station

So can humans still kill me on PvE server? It's origins zombie nation.

Yes. People can still kill you in pve.

So can humans still kill me on PvE server? It's origins zombie nation.

Keep in mind that Mission Guards and Sector B Guards are still a threat, also keep in mind that on the small Island Krk are always Bots (You need to know that if you want to go to Novistrana)
If it was the brigde from Veditch to the bigger Island there is a high chance that he got killed by the Mission Guards from the Ambush Mission.

Also you should know that there are no real Origins PVE Servers! It's basically just a indicator that the Admins want no PVP on their Server. So just because the Server has PVE in his name, don't think that you can't get killed by other players, and the other way around. But of course killing someone on a PVE Server is forbidden and the Admin can ban that person, but still you can get killed by players.

On a PVE server, the general rule is do not kill other players, do not steal and do not base raid. Unfortunately there are trolls that go to EVERY server, even PVE servers, and act like ass hats because they have nothing better to do and find it entertaining. It is possible that you were killed by an NPC. The NPC Hueys/Hind will land when they run out of fuel and the crew will get out and start wandering the map. If there was a mission near by, you probably tripped the mission and got killed by a mission NPC. Sometimes NPCs like to wander off from their mission location as well. I've seen the "Plane Down" mission SUV up in Gord, Novistrana.