...in RoE nothing is ever certain...and although the player version of the domain descriptions does contain info on main NPCs - such as levels and alignment - don't be sure that it absolutely 100% correct. It is what your regent thinks is correct. So that loyal retainer of yours, listed as LG, might not be so holy after all.
Also remember that alignment isn't personality; it's a rough guideline. So if your loyal vassal is NE, that doesn't mean he's in league with the dark powers and is ready to murder you in your sleep. And that LG captain of the guards - he's perhaps a little too zealous, and might actually have a conflict of loyalty between you, the regent, and the local temple.