Yeah Richard, these are actually intro characters. The idea is not to have them fight a deity, just thwart their plans, even if its alerting the other gods as to what is going on.
The machine itself can only be used by a God or demi-God. Part of the design is that it forces the deity to step into the material plane. The machine cannot, for instance, be transported to the Outer plane, because the crystalline matrix "battery" that it uses can only be powered by the souls of the lesser beings, primarily humanoid in nature.
Lamashtu has actually deceived Pharasma by altering the time stream where she gathers her visions into thinking that a cataclysm will happen in the next year or two which has two possible outcomes: humble the mortals of Golorian into realizing their mortality, resulting in wars and petty squabbles/crimes set aside and the majority of the population turning to the Gods of Good, or two, demons pour out from a portal to the Abyss and enslave humanity to serve evil. Good ruse since that's what Lamashtu plans to do - distract Pharasma's attention when the machine is ready to use, jump into the mortal realm, use the machine to bend the Material Plane to her will, then jump back out.
Lamashtu has one of her worshipers leave the plans for the machine somewhere for one of Pharasma's followers to find it, Pharasma decides that it is for the greater "good" to keep the balance and not let Good or Evil triumph for an extended period of time, sets to work building it and gathering the souls of the dead discreetly to power it. Along the way our heroes slowly unravel the plot and have the option to deal with this threat how they will. I suppose if they decide to try and destroy Lamashtu on their own, it will be a fun TPK. :)
A misfunction in the device is probable though, since its all theoretical. They only have plans, no one has had the resources to build it.