Basically, start rewarding things for assists (partial flag returns), pickups, returns, bonus for killing someone within a particular rage of your flag carrier, flag saves,etc.
Similar things could be added to AB. Killing people within vicinity of the flag, flag saves, captures,etc. I know some of these things are recorded in WoW already, but as a separate footnote to your "score" of killing blows.
Things like BattlegroundFu only list your kills/deaths,etc on the FuBar portion (other stuff is a mouse over), which for people concerned with their score only promotes going out and playing deathmatch. The default wow scorboard is the same, sorted by kills. If there was one "score" that included kills but was also modified by these other statistics, maybe those people who actually look at the scoreboard would do things to make that higher instead of just getting one point at a time for kills.