Plot doesn’t continue after killing Darko

It's... not that sort of game. Some of the missions explicitly require you to kill one or more people - including unarmed people. It's disconcerting, yes, but I'm pretty sure there's no way to advance the plot without doing these kinds of missions. The GTA series is infamous for the terrible things you do - it has missions in which you beat up juries, missions when you distribute drugs to kids, missions when you bury people alive, etc.

Alternatively, you can forget about the main plot entirely and just play the game as an open-ended sandbox, taking jobs as paramedic, vigilante, competing in races, etc. (though you have to kill some people just to unlock those options...).

One final thing, if you want to avoid running over pedestrians during intense car chases, use the horn! Pedestrians will run away and jump out of the way when you honk. It's also useful for warning other cars - so useful, in fact, that I've bound the horn to one of my mouse buttons (playing on the PC).

Steam has built-in support for letting you specify command-line args for games.

Right-click the game's entry in the Library and click Properties. On the window that pops up, there's a button named "Set Launch Options...", and clicking that gives you a textbox that lets you type in command-line arguments that Steam will use when launching your game.

You can include the entries you would've had in commandline.txt in there (all on one line, of course, since the textbox in Steam is one line only).