You can tell someone's growing more evil and not really care. Or you can just go along with it. The Gerudo's were theives, and Ganondorf was their King, so they were to obey him (hence calling him the Great Ganondorf). But when he entered the forbidden pyramid, that broke one of their most sacred laws, so they would have made him an exile.
They all speak very derisively of him, however. Let's also put the above quote in greater context:
"That child is destined to
be the mighty guardian of
the Gerudo and the desert.
But this child, its heart
grew twisted with every
The child became a man
who hungered for power
at any price."
The child (Ganondorf) is clearly meant to become important. The guardianship is clearly a revered position within the Gerudo, hence they call it a "mighty guardian".
But, and this is key, when they say that the child grew twisted, they say "But this child..." But. But obviously signals a shift in their view of the child. If becoming twisted were a good thing, they wouldn't say "He's going to be the guardian. But he grew twisted, isn't that good?" Nope. They'd say something like "He's going to be the guardian. He's already grown so twisted, isn't that wonderful?" No but.
Also note this statement:
"To have a criminal such as
him enter... His presence
stains its holy ground."
"Criminal such as him" is the operative phrase here. Note that while they already despise him for entering, they call him a criminal when describing him entering - he was already a criminal before he entered. Now sure, the Gerudo are criminals by nature, and they view that as a good thing, but they also have their own laws and customs, and they say "criminal such as him". This implies a certain distinguishing quality between a typical Gerudo criminal and Ganondorf. They view him as a criminal by their standards, not by conventional standards. That's bad.
All this to say: they hated him before he entered the pyramid, and that action led them to outright exile him. That is a very different story than the Ocarina Ganon, thus - two different Ganons.