Well you are of course right to suggest in your question that robbing Voldemort of his mortal body isn't a bad plan; he could not be a general, he could not set about acquiring the Elder Wand, he could not lay his plans.
But it would not kill him, it would just leave him bodiless once more. But this time, this time his Death Eaters will not believe him gone, this time Wormtail knows what to do to resurrect him. Is it worth risking Snape's life for this minor delaying tactic?
Well, clearly Dumbledore and Snape don't think so, and I would agree with them. Snape is the spy, the double agent, the man on the inside, without him, Dumbledore, Harry and the entire Order are much worse off in the long game.
That's one part of it. But a second part of it is that it is not actually all that easy to kill a man. It's harder than you imagine. The enormity of the act. Making sure your aim is true, choosing your time, your weapon, making your escape. This is why real life assassinations are very carefully planned and many of them fail. Think of Castro and the veritable legendarium that his built up around the attempts on his life. Could Severus Snape presume to surprise Voldemort alone and just fire off Avada Kedavra and get it over that quickly? Not obviously. Voldemort is not very often in such a vulnerable position.
[S]he had no wand upon her either ... how stupid they were, and how trusting, thinking that their safety lay in friends, that weapons could be discarded even for moments ...
Harry Potter and the Deathly Hallows - p.281 - Bloomsbury - Chapter 17, Bathilda's Secret
[I]t had been a grave mistake to trust Bellatrix and Malfoy: didn't their stupidity and carelessness prove how unwise it was, ever, to trust?
Harry Potter and the Deathly Hallows - pp.444-5 - Bloomsbury - Chapter 24, The Final Hiding Place
'...You will hear many of his Death Eaters claiming that they are in his confidence, that they alone are close to him, even understand him. They are deluded. Lord Voldemort has never had a friend, nor do I believe that he has ever wanted one.'
Harry Potter and the Half-Blood Prince - p.260 - Bloomsbury - Chapter 13, The Secret Riddle
Once he has his body back, he does not have around him trusted assistants who could sneak up and kill him in his sleep.
And what if he should be vulnerable for a second? The creak of a floorboard, Voldemort turns around, the curse just misses, and then what does Snape do? Well, I'll tell you what he does, he dies, that's what he does :P
But perhaps you're not convinced, so I'll add one final thing. Tom Riddle can read minds.
'[...] The Dark Lord is highly skilled at Legilimency -'
'What's that? Sir?'
'It is the ability to extract feelings and memories from another person's mind -'
Harry Potter and the Order of the Phoenix - p.468 - Bloomsbury - Chapter 24, Occlumency
And Tom Riddle is so accomplished that he can do this without even looking at the person.
'[...] And I'll tell you this, too,' he added, on a sudden inspiration, 'my wife knows I'm up here, and if I don't come back -'
'You have no wife,' said the cold voice, very quietly. 'Nobody knows you are here. You told nobody that you were coming. Do not lie to Lord Voldemort, Muggle, for he knows ... he always knows ...'
'Is that right?' said Frank roughly. 'Lord, is it? Well, I don't think much of your manners, my Lord. Turn round and face me like a man, why don't you?'
Harry Potter and the Goblet of Fire - pp.18-9 - Bloomsbury - Chapter 1, The Riddle House
Now, it's true, Snape can close his mind. But can he kill his own master, Tom Riddle, without Voldemort noticing? I wouldn't bet my life on it? And recall, Avada Kedavra requires a strong bit of magic behind it. It seems to be perhaps the only curse that cannot be cast non-verbally. You can't just kill someone like that.
'Avada Kedavra's a curse that needs a powerful bit of magic behind it - you could all get your wands out now and point them at me and say the words, and I doubt I'd get so much as a nose-bleed. But that doesn't matter. I'm not here to teach you how to do it.'
Harry Potter and the Goblet of Fire - p.192 - Bloomsbury - Chapter 14, The Unforgivable Curses
'Never used an Unforgivable Curse before, have you, boy?' she yelled. She had abandoned her baby voice now. 'You need to mean them, Potter! You need to really want to cause pain - to enjoy it - righteous anger won't hurt me for long - I'll show you how it is done, shall I?
Harry Potter and the Order of the Phoenix - p.715 - Bloomsbury - Chapter 36, The Only One He Ever Feared
And these necessary emotions that you must summon up can be read by a Legilimens.
You could try and stun him first, I suppose, or something like that. You could try. But your fear, your nervous excitement. Maybe Snape is the one person who could keep it down, but surely Tom Riddle is the one person who could notice. And it's not as if he spends much time in the company of Severus Snape. And I'm sure he's never wandless, never unable to notice Snape attempting to draw his wand, never with his guard down.
Which means that Snape assassinating Voldemort would never be the plan - it's too high risk. Which means that he wouldn't be looking for opportunities. Maybe, in all the years when Voldemort had a body there were times when a man looking for an opportunity to kill Tom Riddle, might have been able to do it, just. But Snape would not have been looking for such an opportunity. He would not have been trying. So he would not have noticed these moments and if he did, by the time he'd thought about it, they would have passed. Voldemort would have faced him once more, would have moved away, would have summoned another Death Eater, or whatever.