Hmm… Except for a few scripted occasions, I’m pretty sure respawns only happen when you change areas. So the respawns really should be a non-issue; the first time through an area should just have the initial spawns and be the hard part. After that you’ll already know the layout and have a clear mission you’re trying to achieve in that area. Which should make it a lot easier to just achieve that specific objective while avoiding enemies.
Are you constantly leaving and re-entering the same areas, rather than entering an area and then thoroughly exploring it in one go?