Well to me it's more like this...
When you are required to play daily or else lose the rewards, it means nothing. People can't always get on daily and shouldn't have to. But when you are given a full week to play, you have no excuses. You can't complain that you didn't get a chance to go for the rewards. So in that respect it's fair.
Competition is only good when all parties are equally met. As the saying goes, fight me at your best not your worst. So just because you win a single day while i'm at work, does not mean you're the "best." But if your guild wins overall for the entire week, then that says something. You deserve those bragging rights. So I think it's fair that the rewards are given out based on the week, not just a single day. Much like a war. You don't win a war in a single day, it's a series of days.
I'm using the term "best" lightly because the game is all about expendable time. And time is the only equal measurement we can have.
And I think you are missing that it's measured throughout the entire week. Nothing has changed except the rewarding. People tend to not care about losing a few battles daily, when they aren't going to lose any rewards daily. I.E defensive/offensive losses now in pvp. In war you can afford to lose a few battles, and still come back to win.