I admit I'm not a big fan of the decision to withdraw Cabrera from the batting title consideration. He has the highest average based on the rules and regardless of what he was using those hits occurred on the field. Since Baseball-Reference.com is pretty much all about what happens on the field, it puts us in a bit of a bind as Cabrera irrefutably (at least as it stands now) has the highest batting average in the league, but the league will not recognize him as the batting champion.
Looking to historical precedent, it's clear to me that we should now and should continue to list Cabrera with the highest batting average in the 2012. However, it shouldn't surprise you that there have been many other cases, though none recently, where the batting titleist at the time and person we currently recognize with the highest batting average don't match up.
The most "recent" case is 1910 where Lajoie had a higher batting average than Cobb, but due to various shenanigans Cobb was given the batting title (though both got the winner's promised automobile).
Likewise in 1902, we list Lajoie ahead of Ed Delahanty. The issues are even larger on the pitching side as the requirements have shifted around before settling on 1 IP per scheduled game (I've seen books citing minimum 10 complete games or 45 innings pitched). Even the 1IP/Gm can cause issues as in 1981 Steve McCatty was the recognized ERA Champion, even though in our opinion Sammy Stewart and Dave Righetti had better ERA's.
To handle this, we've decided to list ERA Leaders and BA leaders as they currently are in the leaderboard pages. These will be updated and change as new data becomes available and we will be apolitical as much as possible in how we draw these leaderboards. This is essentially the status quo.
In addition, though, we will add as awards the Batting Champion and Pitching Champion which will represent the player recognized at the end of the year as the top hitter and top pitcher. And we will strive to denote on each when the winners of the two do not match up.
This way folks can see who was best on the field and who was recognized as such at the time when the season ended.