Yes, yes, we have this glorious JIP system you say! Well sorry, but in objective games, this doesn't cut it. Especially in dominion where your team can instantly lose the game at any time. At least in objective games, being down a player at any time, for any length of time is very detrimental to your chance of winning.
Also, so many times people just leave when the enemy scores the first flag, or when they get a little bit ahead in oddball or koth, and why not? Theres no reason not to, let some other poor sap have to join and play a losing game.
Nobody likes joining a game that literally ends as soon as you get in. But they can't change this, why? Because then the leaving problem will only get worse. If they make it so that you can't join a losing game, or games over 50% done, then at that point, if their team is losing, even more people will just leave, especially if someone else leaves first.