I am probably wrong, but I think the Mord's Disjunction spell can be interpreted to mean that spells and items are not automatically negated.
The phrase in the spell “ending the spell as dispel magic does” could mean that caster level dispel checks are required.
Also, the spell Guards and Wards has as its last paragraph:
"The whole warded area radiates strong magic of the abjuration school. A dispel magic cast on a specific effect, if successful, removes only that effect. A successful Mordenkainen's disjunction destroys the entire guards and wards effect."
The phrase “A successful Mordenkainen's disjunction” suggests it can fail, which is only possible if a caster level check is required. I can't make sense of this phrase any other way.
So, with this interpretation, MD is still a powerful spell: it attacks every target within its area as a targeted[/] dispel magic, and items which are overcome and fail their saves are destroyed.
Unlike Greater Dispelling, it isn't limited to 20th caster level, so epic level casters can use it to great effect.
