On the level "Unnatural Disaster" (level 7, second part of Sintek chemical plant), you have the secondary objective to keep alarm from being raised. This seems to be impossible after you get to the point where you see a scientist which JC informs you has a security card you need to get. The scientist in question runs away and raises the alarm almost as soon as you see him, and is on the other side of unbreakable glass. Does anyone know how to prevent the alarm at this point?

Hey there,

I also asked myself the question, and from a walkthrough I found (link below) which addresses this issue it seems that it is indeed impossible to avoid failing this secondary objective.

https://gamefaqs.gamespot.com/pc/39787-sin/faqs/15778

Bad design there, I guess it must have escaped the developers' notice when they rushed the polishing phase of the game in order to beat Half-Life to the market.

Have anyone checked if it's still an issue after the patch?

If by patch you mean the last official patch, then yes it is still an issue - but well it doesn't really matter, just inelegant.