And asides even if its not going to be as heavily used, why mix the two and risk spreading confusion. If 40K games are a part of the site (which they clearly are) then there needs to be the clear separation and equal representation.
Otherwise you end up under supporting one aspect, which in turn makes it less and less popular. In addition you can confuse your primary market because suddenly there's 40K rules talk in the "rules" section. (a major problem at any time, but especially so when the rules books change and everyone is only just getting their feet steady with a new rules set)