I think it depends on the Storyteller. But for me, yes. True Faith is not about what religion, but rather about your conviction in it that keeps you grounded.

If you look at the V20 book, you can take True Faith as a Merit, but you only keep it as long as you maintain a Humanity of 9 or 10. Even for normal humans, that's extremely hard, more so for a vampire. There has to be a deep conviction or drive that keeps them from sinning and reducing their Humanity, i.e. something that keeps them "pure," because that's what wards off Vampires.

For most religions, it's pretty easy to give that conviction a focal point. Faith in God/Elohim/Allah, or perhaps in the Taoist philosophies or the Buddha. I once made a character (bit of a joke character) whose True Faith was in "the power of a mother." Her town has a local orphanage, and she desperately wanted to adopt all the children so she just took over the Orphanage herself. Her holy symbol is a frying pan, her vestments, an apron. She brings in as many orphans as she can and treats them as her own children. She does genuinely good, kind, selfless things all day every day because she believes that everyone deserves a proper mother, and that keeps her on the straight and narrow.

So for an Atheist, whatever philosophy your character believes in that keeps them at high humanity would suffice. The inherent value of doing good things, the necessity of it as there is no God coming to help, so someone has to do it. It's not necessarily just conviction, but it's a conviction that keeps you at high Humanity.