WI: All Astartes are decimated during the Great Scouring. No new Astartes can be made

If both the Traitor and Loyalists Legions were obliterated during the Great Scouring (Horus Heresy part 2) how much does it hurt both the Imperium and Chaos?

How would it affect how both sides fight with each other, itself or other factions?

Who suffers the least, Chaos or the Imperium of Man?

How would it affect Wh40k?

That's a big hypothetical.  I don't think there are any canon answers, so I will give you my thoughts and speculation instead.  I'd go so far as to say the Imperium of Man is screwed.  Hypothetically you even the playing fields between the Imperium of Man and Chaos, except that Chaos also has daemons, which are usually depicted as needing some sort of super-space-marine to defeat (or maybe just Jurgen).  Perhaps Psykers step up to fill this roll and keep them even?  What about the fact that Chaos can reconstitute certain Chaos Space Marines, bringing them back from death (looking at you Eliphas)?  Surely the power balance of loosing space marines can never truly be mutual.  

Even if you somehow manage to balance out the power of the Imperium and Chaos, then you're just running out the clock until the Tyrannic Wars.  Without the Space Marines (sadly) the Tyranid surely overrun the Imperium, because the Guard held the line - but the Space Marines poisoned the Norn Queens (in at least one of them) to win that war.  Or until the Necron start waking up, or the Tau start invading from the Eastern Fringe.  In many ways, Warhammer 40k is at it's best when it's carefully balanced-out and no side has a real advantage.  By removing Space Marines you don't remove the malevolent threat that Chaos possesses as a story potential, but you do start to hamstring the Imperium of Man unless you bring something else to fill that void.  But once again, this is all just speculation and none of this should be taken as absolute.

Actually, Amathar, you're wrong there. Asked as it is, it's an easy question to answer.
If both chaos and Imperium would have lost all of their Legions during Scouring, the chaos would be lesser for this.
Some reasons:
1. Grey Knights that were never a Legion, thus will remain, and likely multiply in the future.
2. Imperium still had all the geneseed stockpiles to recreate their Marines. It would be slow and painfull process, but it would be done.
3. Chaos would loose their eternal unrest they so desperately crafted with Horus Heresy.

Answering other questions- it would hurt both sides a lot. Chaos gods have a lot thrown in with CSMs, and Imperium Astartes wouldn't go down without a fight. The losses would be tremendous.

How would it affect both sides?
Chaos would loose the Heresy in the aftermath, Imperium would rebuild, a new age of peace would reign and chaos would loose all power, because at the time there would be no one to fight with the Imperium and fuell the gods.

How would it affect 40k?
With chaos pretty much out of the picture at this point, we would concentrate on other races. Eldar have their war with Slaanesh going on, Tyranids are still around nomming everything on their path, Necrons search for new bodies for themselves, and Tau stumble around like blind children. Although at the time we probably would have Pax Imperialis on our hands...

Part of the header question stated that no new Astartes can be made.  I assumed this extended to the supposed "Emperor's Gene-Seed" as well as Chaos, mostly as a balancing at.  I'm standing by my statement (however wrong it may be).  I also stand by my point that, it's all speculation anyway.

I assumed the "no new astartes can be made" was added as an information that there's no geneeed to implant left, because there's no astartes left to be taken from, but there was a hidden chapter at the time, and hidden stockpiles at the time, so they could be made even if every living legionare dropped dead at an instant with his geneseed spoiled.

A fair counterpoint.