I've not had the issue, but for as much as I love RtCW, the stealth levels are real bad. You might be able to get better answers in the Wolfenstein subforum. How are you playing? Vanilla, Unofficial Patch, or ioRtCW? If it's the UP or ioRtCW, you might want to check their sites to see if anybody's having a similar issue.

I think you need to do it in a way that the last guard doesn't see any of his allies being killed (or that he doesnt find anything suspicious).

I played a lot of this game and know exactly what you are talking about.

It means that the last guard is in an "alert" state, meaning he is suspicious (seen somebody die, saw you but not long enough to engage you/initiate alarm). If you look at him, he will not be in his idle/relaxed animation, but will be looking around with his gun raised up. That is unfortunately enough to count as a triggered alarm. The only thing you can do is restart/reload a bit back and do it without him becoming alert.

It mostly happens when you shoot the guy on the tower when the gate guard is looking in his direction. That causes him to go alert. You either have to snipe the guy on the tower when the gate guard is not looking, or snipe him when he is hidden from the sight of the gate guard. Also be absolutely sure you do NOT use any non-silenced weapon in this mission and no enemy manages to get a shot off. The loud noise might alert somebody, once again counting as an alarm. Especially in the last complex (like an officer getting one shot off). The moment the gate guard hears anything at all, it is instant mission failure (which you get to know once you reach the truck).

Also be 100% sure to avoid line of sight with the final gate guard (e.g. when you are walking around the complex, picking up items etc.).

I snipe the guard in the high tower from the hill and i do it in a way that i wait for him to come to the spot where he is not visible to the last guard.

Yes, as I said, that is the best way to make sure that the gate guard doesn't see it (when the sniper is behind the top of the water tower).

It's used in the real world:

https://en.wikipedia.org/wiki/Wolfenstein_%28rock%29
https://en.wikipedia.org/wiki/Eugene_Victor_Wolfenstein
https://en.wikipedia.org/wiki/Lincoln_Wolfenstein