Is playing this game through Arx Libertatis the best way to play this game or should I just play the untouched GOG version?

This depends on you, I would prefer Libertatis as the original release has given me a lot of issues and was unplayable.

Is there a way to get rid of the magic-rune-drawing-system? Maybe through a mod or something?

As far as I know there isn't any way to change the magic system. I know it's a huge pain when starting out but if you stick with it you'll get the hang of it.
One good thing about the game is that you can find scrolls for the spells you'll actually need to play. Find a scroll, put it in your quick cast slot and you won't have to worry about drawing the runes.

I hated the rune drawing when I first starting playing Arx but with some practice I ended up loving it and just finished my 3rd play through of the game. This time I went pure mage and handled every enemy in the game easily ( except the beast in the dwarf mines of course ) with spells.
It was actually -too- easy as a pure mage and I wouldn't recommend it to anyone unless they just want to play through for the story.