Landing next to the base and not attacking it but an enemy unit.

[Glorishears]

You're right that killing a runner right next to your opponent's base is often a bad trade -- your runner is worth more than his (his: 1 to spawn, 1 to move once, 2 total; yours: 1 to spawn, say 3 to move across the board, 4 total).

BUT

By the same token, 5 wit (4 to get the runner there, one to hit the base) can be too high of a price to pay for one base hit.

There's discussions up and down the forums about whether the first player has too much of an advantage because they get five wits before the second player does anything. Just 5 wits.

If you're going to try to win by runner-sniping your opponent's base, you're giving up SIXTEEN WITS before you end the game with that fifth hit - 4 hits * 4 wits per hit (5 wits to get each hit minus one wit for your opponent to kill your runner).

Sixteen wits is enough on many maps for your opponent to completely block their base with soldiers. By the time you come in with your last runner trying to finish them off, that army of soldiers will be advancing at you in lockstep and you won't have anything to kill them with.

So, no, it's not good to trade runners deep in your opponent's territory. But it's not good either to trade a runner for a single base hit, either.

Buffing your runner helps. You may be able to trade one advanced runner for two of theirs, and that might be worth it (or for two base hits).

Killing healers and especially snipers helps. A sniper "next to their base" might still be 3 slow moves away from the spawn -- that's worth 6 wits, and is totally worth trading an advanced runner for, not even counting the initiative advantage you'll probably get.

And this is why runner rushes ARE popular on Long Nine. There's more spaces a defender needs to block and they're farther from the spawns, so building a wall of soldiers costs more than it does on other boards. Not only is it relatively easy for a runner to get from spawn to enemy base, there's lots of space up and down the board, making it easier to dodge any sentries along the way.

Even on Long Nine, given a choice between a single base hit and killing that sniper, you take out the sniper.

And all this has been without thinking about initiative, visibility, opening a path for another unit, or any other considerations. With those in mind, sometimes you should kill a runner rather hit their base.