I have personally yet to participate in an actual tournament, only big game day events where its just a free for all of playing 40k. Although I've been in enough tournament atmospheres to understand your argument. Hobby shops will always have different "add-on" or soft scoring rules depending on their history of hosting tournaments. One hobby shop I go to doesn't have much of the soft scoring in their rules, where as another does because there had been problems in the past with overly-competitive players, so they wanted to reward the players with good sportsmanship. There is even one hobby shop that has a store wide rule asking people to practice good hygiene. Yes its actually there because enough lazy slobs play in Friday card game night and all come together as if performing a ritual for Nurgle (we have learned to never go there on Friday nights
Now as to your points, I agree with most of them. It does suck that you can work extremely hard practicing your tactics and reworking your list down to the last point and someone could beat you by a few points based on the Refs "opinion" of another players well painted army or sportsmanship. I think that painting should be judged in a painted army contest as just an add-on to the tournament and not part of the scoring for the games themselves. I personally haven't had much time to paint my army at all, even prime them. So in tournaments where a well-painted army affects my scoring, I'm already at a disadvantage. ALTHOUGH, it brings up my main point, Rewards vs Penalties.
As you mentioned, most sports these days go by the "punish with penalties" way of dealing with negative actions and behaviors. Which most of the time, because of the nature of the sport/game, it has to be that way. Your right, we can't give extra points to football players who make good clean tackles versus someone who still made the tackle, but wasn't as "perfect." Plus most tackles are done with multiple players tacking down one guy so figuring out those points would be.....well I'm trailing off, back to the main points. At its core, 40k is a HOBBY with the main 3 facets of Building, Painting, and Playing. Not to say it can't be competitive, it definitely can be, but playing the game isn't everything this hobby is about.
Now think about it as a hobby store owner. Lets say you set the tournament rules like you want, negative consequences for negative actions a.k.a. penalties. The rules are set that it can eventually escalate to the player getting banned if their actions continue. Yes this can work, but no good comes of this system. A player gets penalized, argues about it for a bit, goes back to game frustrated. Maybe the player gets hit with another small infraction because of some bad sportsmanship, more arguing. Arguing can eventually lead to some tempers flaring and finally the thought of banning that player. That is a lose lose scenario. You have lost a player to your store, the other players in that community may have lost a player, and possibly that player is more likely to stop playing.
With the current, more frequently used soft scoring, it provides positive reinforcement to the players. As I mentioned, I don't have a painted army, but if I think I'm going to participate in a tournament with soft scoring dealing with painting, I'm more likely to actually paint my army and have it look cool. I'll be more motivated to actually participate in all facets of the hobby itself. As well, from what I've been told, sportsmanship "points" or rewards are mostly decided on after the match or near the end of the tournament, whereas penalties are mostly done during a game. We all know if we were deducted points after the match because we said something insulting its going to become a giant argument of "he said - she said." Plus can you imagine getting penalties in the MIDDLE of your games. That can completely throw off your mind set and change your attitude for the night.
Overall, its definitely a good argument to bring up, but I think the common way hobby shops have been running tournaments with soft scoring is a lot more fun to play in than tournaments that would just penalize the players. It would just have a negative feel about it. Yes, the Refs still have the overall opinion of good/bad sportsmanship, but that comes down to your experience in that hobby shop and if you feel the Refs are trustworthy and unbiased in their decisions. If I were to run a tournament personally, I would have the tournament with a side painting contest and would reward good sportsmanship during the tournament with small prizes, BUT it still wouldn't factor into the final standings of the tournament. If someone becomes enough of a problem consistently during the tournament or in multiple tournaments, they will be dealt with.