It all depends on positioning. If the Sanctus and Lilith start "face to face" (purely from the angle, not distance) the Sanctus has very bad chances in an unscripted battle, due to the Sanc first shooting at the laserturrets on the Lilith' "claws". If both beamsalvoes are spot on, the Sanctus is dead.
But if the Sanctus starts a bit below the Lilith, it sometimes manages to take the turret out and afterwards easily win.
Also if the Sanctus can get above the Lilith, that takes her out of the firing arc, which also spells doom on the Shivan cruiser.
In a scripted battle, where the Sanctus aims all it's weapons on the beam turret, my money would be on the UEF, no matter what angles they start off from.