As far as I'm aware, SMG had signed a five year contract, so even if she HAD wanted to go off and make movies, she had no option to do so, being tied contractually to the show for at least five years.
Had she wanted to take off, I'm sure that she and Joss would have been able to come up with something, but seeing as how we know that Joss had much of the character's storyline already mapped out, I doubt he would have been okay for his lead actress to just take off.
I like Faith, I do, but I don't think that Eliza was a strong enough actress, nor the character big enough, to take over the show in S3. Certainly, in S7, when she had time to grow, I could have seen her having her own show, a spin-off. But not at that point.
Plus, Faiths' arc in S3 was definitely not the kind of arc for a lead character. IF she had taken over in S3, the rest of the show - or at the very least, the next two seasons - would have been more about Faith trying to redeem herself for what she did in S3, which, given the time frame, would have been far too much like AtS.
