The Engineers that planet seeded work on a very long timescale. Thousands of years between visits.
So..a 100 years or so of humans reaching some of their planets is nothing.
They could retaliate 10,000, 100,000 years later.
Or they may already know through experience that humans will self destruct or that the alien creatures will eventually become widespread.
There does seem to be different Engineer factions or varieties.
If this is "end" of them, they seem to have regressed and depopulated to just one city perhaps without the kind of technology that might be expected. So maybe their civilization collapsed? Or maybe those remaining are like mountain people living simply. The others may have moved onto other planes of existence ala 2001 or Interstellar or The Matrix.