First off, the character who told Tommy not to worry about art wasn't Miss Emily, but Miss Lucy (Lucy Wainwright). This matters because Miss Emily was the Head of Hailsham, while Miss Lucy was one of the guardians (something like a coach or phys-ed teacher).
Miss Lucy was dismissed from Hailsham right after her second meeting with Tommy, the one where she reversed her earlier advice. Miss Emily explains near the end of the novel that Miss Lucy felt the students should be told clearly what awaited them after Hailsham. The administration disagreed: they wanted to shelter the students from this grim knowledge. Miss Emily says to Kath and Tommy years later:
Lucy was well-meaning enough. But if she'd had her way, your happiness at Hailsham would have been shattered. ... you wouldn't have lost yourselves in your art and your writing. What should you have done, knowing what lay in store for each of you? You would have told us it was all pointless, and how could we have argued with you? So she had to go.
Miss Lucy's first meeting with Tommy occurred when he was in a bad way at school. The other students teased him mercilessly for his lack of artistic ability, and he responded with temper tantrums and childish drawings, which just led to more teasing. Miss Lucy's advice--don't worry about "being creative"--helped him break out of this doom loop. In this she showed empathy and perceptiveness. Even if Miss Lucy had believed in the school's mission whole-heartedly, she must have recognized that in Tommy's case, it amounted to shoving a square peg into a round hole.
But very likely Miss Lucy already had her doubts. Sometime after this first interview with Tommy, she addressed a whole group of students, spelling out their fates in explicit detail:
...none of you will be film stars. None of you will be working in supermarkets... before you're even middle-aged, you'll start to donate your vital organs. That's what each of you was created to do.
Why did Miss Lucy change her advice to Tommy just before her dismissal? The book does not provide enough info for a definitive answer. Perhaps the administration had recently learned how her actions were undermining the school's mission (as Miss Emily must have viewed it); maybe Miss Lucy was making a last desparate attempt to save her job. Perhaps Miss Lucy had recently learned the purpose of the gallery (though this seems at odds with an earlier passage).
Or finally, Ishiguro has said that the clones of Never Let Me Go are a metaphor for ourselves. So perhaps Miss Lucy had come to feel that art still has a point, even when faced with the inevitability of death.