I play with the cursor keys instead of wasd. Doing this since 20 years and won't change it for this game.

I can reassign any key, but not the key that commits the vats actions (e). It doesn't seem to be reassignable. Can this done by the ini-File in some way?

I had no problem reassigning the E key in the game. The only key it won't let me change is the 2 key which is hard set for changing ammo types.

The keys used in VATS screens, inventory screens, barter screens, etc. are not mappable, and don't remap with the E key when you change your keybinds. I usually get around this by simply clicking Accept with the mouse instead of using a key.

EDIT: I had no trouble reassigning '2' in the keymap menu, although I haven't tested it in-game yet (don't have any alternate ammo types to try it with).