Morrison did "Something" like that during Batman & Robin. Where Joker laced Joker venom under his nails, and whomever he scratched, would be poisoned. It was in issue 13 of that series.
I want to see Snyder's story pan out, and then, take Joker off the table for about 2-3 years, and have him return when he's had time to be missed. I think part of the problem right now is, there's so many Batman books these days, it's hard to actually have a good villain off the grid for a while for readers to miss them. And with a character like the Joker, who every writer can adapt to their own styles, it's hard to keep him away for long.
This has been done a number of times in the recent past, tho. He dissappeared after he was shot in the face at the start of Morrision's Batman run. He dissapeared after Damien ran him over at the end of Batman R.I.P. He was missing during most of the Batman Reborn arc until the end of Morrison's Batman and Robin run. And he was gone for a year after 'Tec #1.
I agree with you in that he should be used sparingly, but he's been taken off of the table frequently in the past 6 or so years.