You need to advocate a position like the one I've staked out several times "In times of disconnects, the player still online default wins." This solves disconnecting issues for winning, but not losing (as losing won't go down... because they have no such penalty system in place).
To solve disconnect problems from losing, it needs to have a "participation" bonus for losers, not a drawback. So, say, it you get 15 points for beating a 1500 player, they should get 1.5 points for losing to a 1500 player. Then, after the battle, you're at 1515, and they're at 1502 (rounds up). Thus, playing and losing over and over again increases your score for the tourney. Meanwhile dcing wouldn't increase your score, so there's your incentive to not dc.
Will there still be DCs? Yeah. Stall teams suck. If you play me with a team full fo stall tactics, it's probably worth my time to DC - I can lose to 3 other people while I'm losing to you. Then benifit of a no-loss scenario is that it advocates playing more games.
MTG uses a similar system for their Arena - 3 points a win, 1 point a loss, players play for X hours, and the most points wins.
Re: Stall teams, I remember the strategy of playing control decks. Your job was to win game 1, then stall out game 2. Time is called, and you win 1:0:1. In the finals I remember seeing he's got a stall deck, and conceeding 1st game. I thwomped him 2nd game, but lost in the third - control tends to beat aggro... especially aggro elves. :P
So stall teams would be a problem for wifi tourneys like this because they're not worth the time to play against. And there's no system I can think of that would make them worth the time to play against unless you massively penalize dcs, which is unfair since some dcs are because of wifi issues.