My league has no policy either way on scooping, but the key thing to consider (for both League Leaders and players) is that the readme document does say: "You may opt to give a player no League points for a match if you feel they are working the system."
In my opinion, there's a difference between scooping early-game when things look hopeless versus late-game when things look hopeless. In the late game, if a player KNOWS his/her deck and has essentially been checkmated (ex. main attackers KO'd or otherwise discarded, and draw engine shut down, no Night Maintenance or Energy, etc.), I feel that scooping is still meriting points, but that is a slippery slope. If you've been checkmated, just fight it out, even if your opponent wins, rather than tipping your king (OK, so that analogy is not exactly identical) in single-game matches.
However, any scoop in early game (e.g. before one player has taken 4 Prizes) should not merit points, in my opinion.
Of course, there is the idea to have this taught for best-of-3 matches, but that should be easy enough to just say, "This would be a point that I would scoop in Game 1 of a best-of-3, but since it's a single game, I'll tough it out."