I found this a pretty cool experience. It really gets your heart pumping, and it is supposed to do so! You are in a pretty serious situation after all.

But yeah, the big, flashing timer is kind of distracting.

Best advice I can give: Ignore the timer. You have more than enough time to search pretty much any building there, pick up items that help you, and wait for a moment if NPCs are positioned badly (so you can't sneak past them).