He did not whip his wand at Harry but at Minerva. You'll also notice that as she steps in front of him (pushing Harry at the same time), he lowers his wand a bit, as if he does not wish to hurt her. That's the reason why he flees after - to hurt o kill nobody.
Besides, he could not tell Harry then about the Horcruxes ! He's supposed to be loyal to Voldemort. Have te noticed the Carrows standing behind him ? And the Slytherins in the Great Hall ? He just could not tell Harry anything that could have shown he was on the boy's side.
I think he only raised his wand in defense of himself--he knows Harry will likely start firing curses, and he's just preparing. After all, Harry has already attempted to fight Snape (right after Dumbledore was killed) and although Snape easily blocked Harry's attack that time, Harry has had a anno to work on his skills (and for his anger to ferment.)
As others have detto above me, it would have been impossible for Snape to tell Harry anything at that point--he was still playing the role of the loyal Death Eater and the time. And considering how angry Harry was, I doubt he would have listened to anything Snape had to say.
He didn't whip it out and point it at Harry. If I remember correctly, he pulled it out when the large number of Order members strolled through the doors of the Great Hall (when Hogwarts was supposed to be on lock-down), and when Minerva stepped inoltrare, avanti against him.
How, exactly, was he supposed to tell Harry? Like LadyNottingham said: they were in the middle of the Great Hall, surrounded da people.