Unfortunately, this is just one of those places where two
completely separate areas of the rules have grown together in
an unusual manner. Historically, golems and intelligent magic
items haven’t shared much (if anything) in common. But as the
rules for golems have made them more like magic items (in that
they’re crafted in a similar manner) and the rules for intelligent
magic items have made them more like golems (in that they’re
considered creatures with the construct type), weird situations
like this occur. Two adjacent branches, but growing from
slightly different trees, and therefore interacting slightly
differently in occasional corner cases of the rules.
Here’s the important distinction: Golems are not magic
items, and Mordenkainen’s disjunction affects only “magical
effects and magic items.” Intelligent magic items are, as one
would expect from their name, magic items (even though
they’re also creatures), so the spell affects them.