Of course Perseus will die at the end of his journey. He's a mortal man, and that's end of every mortal man's journey. Just give it a couple of decades...
The three hags' recommendation that Perseus use Medusa's gaze to defeat the Kraken has a secondary advantage that's not as obvious in the first film, when he and they weren't quite as hostile to one another. Because they're blind, the hags are immune to Medusa's gaze themselves, so if Perseus bears a grudge against them for trying to sacrifice one of his men, he can't turn it against them like he could, any other weapon they might have suggested.
The snakes on Medusa's head keep writhing and hissing after she's decapitated, which explains how Perseus was able to safely find the darned thing after killing her: he closed his eyes and listened.