"A mob jumps on their feet" - is it positive remark (i.e. mob is cheering him) or negative (like they are in anger?)?
The word "mob" is usually negative -- it's often used in reference to the Mafia, or to lynchings, or to pogroms, etc. You could say, for example, "The mob of Germans cheered and yelled approval for Hitler." HOWEVER, in this case, the "mob" is not responding to a leader/dictator who's standing at the podium on stage:

And as you step back into line
A mob jumps on their feet
The image that comes to mind is that someone within the leaderless mob whispers "Hey, it was probably the JEWS who threw the bomb at Alexander II" or "I heard from Bill Smith who heard it from Harry Johnson that he saw a BLACK MAN near the place where the woman was raped..." The rumor spreads and the "mob jumps on their feet" to start a pogrom or lynching, and the person who started the rumor "steps back into line," disappearing into the crowd. So your interpretation of "shadow manipulation" is exactly right.

"See the lightning in your eyes"
I would understand this to mean "if they looked more closely into your eyes, they'd see your dangerous nature." Keep in mind that "lord of the flies" could suggest the Hitler-ish young boy Jack Merridew in the William Golding novel, or it can be a nickname for Satan himself.

"Take him out today" - does it mean "kill him"? Hasn't he already killed "him" in the previous quatrain?
Yes, it means "kill him," but here it doesn't necessarily have the force of a literal imperative referring to a near-future action. You could interpret it as "you have killed another today, as you habitually do every day."

"Slowly out of line"
I think this means that the potential victims are gradually beginning to panic, which will cause them to make a fatal mistake.