Yes, the drowning is disturbing, but it's such an appropriately anonymous way for someone who sought the spotlight and power to die. Seeing Peter finally decide that even death was better than his situation does go some way in redeeming him. One does have to wonder if Tom would draw on his horcruxes to stay alive and wipe them out or if he'd become a wraith once again; personally, I prefer the first one as that eliminates a lot of problems (though I could see it temporarily giving Harry quite the ehadache) and make Halloween, 1981 the fulfilment of that prophecy.