This question started out asking whether a no-magic, no-upgrades pacifist and ghost runs are possible at all, but now that it seems to be confirmed as impossible, I'm expanding the scope to be more specific.
How many points are there in the game that absolutely require the use of magic (notably blink) or any of the mobility-enhancing upgrades, such as Agility, to progress?
In addition to the above, how many runes, bone charms and Sokolov paintings require such to obtain, as well?
And finally, how many points are impossible to slip past the guards unnoticed without such methods?