These are my suggestions for using a Thousand Sons army in the Pre-Heresy period.
I would recommend using Codex: Chaos Space Marines to represent a Thousand Sons army, though my Thousand Son army will be based before the Council of Nikaea, or during the period immediately before the Heresy began when Magnus began ignoring the rulings of Nikaea.
I would use the Chaos Marine Codex firstly to represent the greater number of Psykers in the Legion - the Aspiring Champion of a unit of Thousand Sons is a Sorceror and as such must choose a Psychic power from the Chaos Armoury. The Special Rules for units of Thousand Sons (Slow and Purposeful, Inferno Bolts, Mark of Tzeentch) could be representative of the Legionnaires methodically advancing across the battelfield, protected by the sorceries of Magnus, bringing the Wrath of the Emperor to the enemies of mankind in the form of psychically modified bolter shells. Also units like Terminators only have access to Pre-Heresy weaponry making theming the army alot easier.
Obviously a degree of control has to be exercised when using the Chaos Codex to represent a Pre-Heresy Thousand Sons army - no Defilers, Possessed, Daemons, Obliterators etc.
Someone on the "Which codex to use?" topic discussion suggested that it would be good to use the SM Codex with Grey Knight allies to represent the prestigious psychic abilities of the Thousand Sons psykers.