The reputation leagues seem to ignore reputation loss due to post deletion. The reputation earned for the same post is counted though, in fact, it seems to ignore reputation capping.

Oliver has an impressive reputation league year 2012 score. It's a bit weird though that it's higher than his total rep — he didn't start out with minus 1676 rep, did he?

I'm not sure what's going on here, but this seems to be mostly a result of the deletion of this topic and the very high score answer by Oliver…

• if we ignore the deletion
• if we ignore daily reputation capping (as is shown in the moderator-only reputation stats)

The June 2012 reputation league score of ~4300 rep seems indicates the same behavior, as it's the approximate sum of positive reputation changes in June recorded in the moderator-visible user profile (ignoring the deletion).