I'm not so sure of that. If there is one thing the HH book series added to the universe that wasn't arguably ill-conceived, it's the idea that the Chapter had previously existed as a maneuver unit within the legions, a unit of approximately a thousand fighting men, somewhat similar to a battalion or somesuch. Regardless, the idea of a thousand fighting men isn't unique to the 40th millennium.
Again, this is one more way the Imperium limits the capability of its various constituent parts. Imperial Guard commanders do not have access to interplanetary transports. Navy Captains and Admirals do not have access to substantial fighting forces to occupy planets, the Ecclesiarchy wasn't supposed to have access to any military forces (they cheated... but their forces still aren't humongous) and finally the Astartes are limited in numbers.
Fact is, we know that marines aren't incorruptible. If anything, the prospect of a marine chapter going rogue or to chaos is such a terrifying prospect that it's better to keep them somewhat limited in the case of them doing so. Chapters who refuse this are either the subject of much controversy, or supported by ancient claims to their organizational body, or somehow working with some kind of "alibi" against corruption. (the Black Templars' constant crusading and lack of a chapter homeworld might count as this, though they still seem fairly controversial.)
Point is; the numbers 1000 is meant as a standing rule, but at the same time, some leeway and turning of eyes is provided on a case-by-case basis. The Imperium Is A Big Place, after all.
In an age when incense is considered a required component of a toolbox, who is to say what kind of mathematic accuracy we can expect?
The reader-response approach to 40k storytelling (i.e. role-playing as a scribe reviewing files from a crumbling, occasionally inaccurate database) has always been one of the most intriguing aspects of the fluff to me. This is the reason I enjoy conflicting versions of events in disputed canon. It allows for discussion and debate among peers as to the "truth". (Much as might "actually occur" in the era before someone pulls a bolt pistol, heh.)
I totally agree that a subjective interpretation of "1000 men" is more my own pet theory developed while reading the fluff than concretely supported by text. I just happen to prefer some subjectivity without imposing on anyone else's world view. To say there are exactly 1000 men per chapter is a totally legitimate stance, although I would prefer the word "roughly" in place of "exactly". If there are significant deviations from these dictates, they probably come in the form of a byzantine monitoring structure of how many chapters that exist at any given time; I highly doubt any but the Emperor actually knows how many chapters there truly are per minute. (Why do people feel the need to make 1000 chapter lists? It's just going to change when warp storm Abbadon rolls in, or seasonal Tyranid showers blow through, or whatever!) Off topic, sorry.
As currently being discussed on another thread, the fans are given many guidelines and options in what to favorably interpret as truth. Anything is possible. Three friends can have four vastly differing conceptions of the scale and type of conflicts they face, and while each are beholden to their own pet theories, they can all share an exciting game with each other. The strength of the 40k setting is letting the players fill in the blanks with their imagination.
My answer is tank drivers drive those tanks, who else?