There are no werewolves in the Forest. Hagrid was just giving a quick, factual answer. He might also have been teasing Malfoy.
I think it's correct to say that there were no werewolves in the Forest for the reasons stated in the question. Primarily, it would've been dangerous for the students; I think we can conclude that Dumbledore was aware that students like Fred, George, Harry, Ron and Hermione went into the Forest when they weren't strictly supposed to. The Hogwarts authorities wouldn't want to expose unsuspecting students to bites from rampaging werewolves at the full moon. Keeping werewolves in the Forest would also be inhumane for the werewolves, although it's worth noting that living in the wild isn't actually out of the ordinary for werewolves.
"However, it has been difficult gaining their trust. I bear the unmistakable signs of having tried to live among wizards, you see, whereas they have shunned normal society and live on the margins, stealing — and sometimes killing — to eat.”
(Half-Blood Prince, Chapter 16, A Very Frosty Christmas).
I initially concluded that there was no canon confirmation on whether or not there were werewolves in the Forest. Robopuppy has since then contradicted me with a fantastic answer from Pottermore which proves that there were merely 'normal' wolves but no werewolves. I think that clears up the confusion as to whether or not Prisoner of Azkaban contradicts Philosopher's Stone. It doesn't; the 'werewolves' in Philosopher's Stone were not real werewolves at all. However, that doesn't explain why Hagrid didn't tell Harry and co that the Forest was a werewolf-free zone.
So the question becomes, why wouldn't Hagrid just say there were no werewolves around?. Well, there are multiple reasons why the unicorn couldn't have been taken down by a werewolf. The variations in speed between unicorns and werewolves is one factor; the lack of werewolves in the vicinity is another. I think that, in Hagrid's mind, he was answering Harry's question directly by ruling out werewolficide on account of speed.
“Could a werewolf be killing the unicorns?” Harry asked.
“Not fast enough,” said Hagrid. “It’s not easy ter catch a unicorn, they’re powerful magic creatures. I never knew one ter be hurt before.”
(Philosopher's Stone, Chapter 15, The Forbidden Forest).
True, Harry has something of a bee in his bonnet about werewolves. He mistakes Ronan for a werewolf just a few minutes later.
“I knew it,” he murmured. “There’s summat in here that shouldn’ be.”
“A werewolf?” Harry suggested.
(Philosopher's Stone, Chapter 15, The Forbidden Forest).
Hagrid likes Harry and so perhaps it would be kinder to simply say, "You know what, Harry? Forget this whole werewolf thing. There are no werewolves around. Capeesh?" Yet I think there are two main reasons why Hagrid doesn't spell out the lack of werewolves to Harry.
Firstly, Hagrid is engaged in a complex and dangerous investigation. He's in the Forest, trying to investigate something he's never come across before (a slain unicorn). He has to keep his wits about him at the best of times in the Forest. To complicate matters, he also has to look after a bunch of untrained first-years. Even if he likes some of the first-years in question, they make his job much harder. At one point he has to run through the undergrowth to 'rescue' Neville when Malfoy plays a prank on him. It would be understandable if he was a little terse when responding to silly questions from someone with little to no understanding of magical creatures. I think Hagrid's response has just a touch of agitation to it. Of course werewolves couldn't be killing the unicorns; they're not fast enough. He likes Harry and usually is happy to educate him about the magical world. But, in this instance, he doesn't have the time to stand around explaining werewolves to Harry when they're in a tense and dangerous situation.
Secondly, Hagrid may be being slightly mischievous. Stress and cheeky humour don't always go hand-in-hand but I think they do in this case. The whole obsession with werewolves in the Forest originally started with Malfoy, not Harry. He begins to panic when Filch tells him where he's going for his detention.
"Well, think again, boy - it’s into the forest you’re going and I’m much mistaken if you’ll all come out in one piece.”
At this, Neville let out a little moan, and Malfoy stopped dead in his tracks.
“The forest?” he repeated, and he didn’t sound quite as cool as usual. “We can’t go in there at night - there’s all sorts of things in there - werewolves, I heard.”
Neville clutched the sleeve of Harry’s robe and made a choking noise.
“That’s your problem, isn’t it?” said Filch, his voice cracking with glee. “Should’ve thought of them werewolves before you got in trouble, shouldn’t you?”
Hagrid came striding toward them out of the dark, Fang at his heel. He was carrying his large crossbow, and a quiver of arrows hung over his shoulder.
“Abou’ time,” he said. “I bin waitin’ fer half an hour already...
(Philosopher's Stone, Chapter 15, The Forbidden Forest).
Note that Hagrid was walking towards them during this conversation and could quite possibly have overheard the last part of it. He knows that Malfoy is a petrified wuss; Malfoy had revealed as much before they went into the Forest.
“I’m not going in that forest,” [Malfoy] said, and Harry was pleased to hear the note of panic in his voice.
“Yeh are if yeh want ter stay at Hogwarts,” said Hagrid fiercely. “Yeh’ve done wrong an’ now yeh’ve got ter pay fer it.”
“But this is servant stuff, it’s not for students to do. I thought we’d be copying lines or something, if my father knew I was doing this, he’d —”
“— tell yer that’s how it is at Hogwarts,” Hagrid growled.
(Philosopher's Stone, Chapter 15, The Forbidden Forest).
I think that Hagrid knows that Malfoy is terrified of the Forest, including the idea that it might contain werewolves. Malfoy isn't actually present when Hagrid says that werewolves aren't killing the unicorns. But why categorically rule out the idea that there might some in the Forest in the minds of the students? Detention is supposed to be a deterrent after all. If word spreads that getting into detention means going into the werewolf-infested Forest then students might think twice before causing trouble. And if that word should reach Malfoy in particular then that would give Hagrid some leverage over him for the next seven years. Harry, Hermione and Neville are the bravery-house; Malfoy was the only real wimp at the detention. I suspect that Hagrid had a wry smile on his face at the thought of Malfoy expecting a werewolf attack at any given moment. It would've been a pity to deny him that fear...