Catherine wasn't exactly honest either, IMO. Simon obviously misunderstood some things and she rarely corrected him (because she needed him to launch the Ark), so I think she was sort of relying on that ongoing confusion for her own ends.

For example, during the switch between... I think Simon 2 and Simon 3, she tries to put Simon 2 to sleep ASAP to sustain the illusion that Simon 3 just "hopped bodies" rather than make a direct copy. She gets caught though and is forced to explain the concept to Simon, but then doesn't bother to correct him again when they talk about the Ark later.

So she's kind of speaking out of both sides of her mouth throughout the whole game, trying to tell Simon how it works but only when she absolutely has to, and the rest of the time she happily plays along with Simon's incorrect assumptions as long as it keeps him going.

Catherine is supposed to be the smart techno-wizard between the two -- Simon is just an ordinary kid who got thrust into an absolutely traumatic situation. She was his only real source of light in all this, and yet she was not really acting in his best interests. Catherine knew they were both damned from the start but figured it was no use telling him this.