Hatred of Muggles would still exist.
Though the Dark Lord lost the war, wizards who hate Muggles would still exist. Wizards hating Muggles wasn’t caused by the Dark Lord, and there’s no reason to think they’d be eradicated by the war with the Dark Lord. A certain amount of wizards have hated Muggles for centuries, predating the Statute of Secrecy.
“A pro-Muggle story showing a Muggle-loving father as superior in magic to a Muggle-hating son? It is nothing short of amazing that any copies of the original version of this tale survived the flames to which they were so often consigned.
Beedle was somewhat out of step with his times in preaching a message of brotherly love for Muggles. The persecution of witches and wizards was gathering pace all over Europe in the early fifteenth century.”
- The Tales of Beedle the Bard
The war wouldn’t have killed off everyone with pure-blood values. The wizards who hate Muggles weren’t all actually fighting for the Dark Lord - some of even the most avid believers in the pure-blood cause just were quietly in favor of the Dark Lord.
“Were – were your parents Death Eaters as well?’
‘No, no, but believe me, they thought Voldemort had the right idea, they were all for the purification of the wizarding race, getting rid of Muggle-borns and having pure-bloods in charge. They weren’t alone, either, there were quite a few people, before Voldemort showed his true colours, who thought he had the right idea about things … they got cold feet when they saw what he was prepared to do to get power, though.”
- Harry Potter and the Order of the Phoenix, Chapter 6 (The Noble and Most Ancient House of Black)
Several wizards hate Muggles, since some wizard parents avoid telling their children stories that paint Muggles in a positive light, like the original version of “The Wizard and the Hopping Pot”.
“To this day, some Wizarding children are only told the revised version of the story by their (generally anti-Muggle) parents, and the original, if and when they ever read it, comes as a great surprise.”
- The Tales of Beedle the Bard
Parents requested the removal of certain stories that were too approving of Muggles, so there is a contingent of wizards who hate Muggles and want to pass their beliefs on. It’s likely at least some of them were successful at this.
“More than one parent has demanded the removal of this particular tale from the Hogwarts library, including, by coincidence, a descendant of Brutus Malfoy and one-time member of the Hogwarts Board of Governors, Mr. Lucius Malfoy. Mr. Malfoy submitted his demand for a ban on the story in writing:
Any work of fiction or nonfiction that depicts interbreeding between wizards and Muggles should be banned from the bookshelves of Hogwarts. I do not wish my son to be influenced into sullying the purity of his bloodline by reading stories that promote wizard—Muggle marriage.”
- The Tales of Beedle the Bard
Also, some of those who did fight for the Dark Lord did survive, and their beliefs didn’t necessarily change. Lucius and Narcissa Malfoy didn’t stop disliking Muggles because they lost the war or changed their minds, they just didn’t want to go to Azkaban.
Georgina: Did lucius malfoy, and all the other escaped death eaters, go back to azkaban
J.K. Rowling: No, the Malfoys weaseled their way out of trouble (again) due to the fact that they colluded (albeit out of self-interest) with Harry at the end of the battle.
- Bloomsbury Live Chat (July 30, 2007)
Perhaps most importantly, there have been wizards who hate Muggles for centuries - there’s no reason to think this particular war would eliminate that from wizarding society entirely.
The Ministry did change, however.
Though wizards who hate Muggles wouldn’t stop existing because of the war, the Ministry did indeed change as a result of the war. It was de-corrupted and its discrimination was eliminated.
Leaky Cauldron: What, if anything, did the wizarding world learn, and how did society change, as a direct result of the war with voldemort? (i.E., not as a result of harry, ron and hermione's future careers.)
J.K. Rowling: The Ministry of Magic was de-corrupted, and with Kingsley at the helm the discrimination that was always latent there was eradicated.
J.K. Rowling: Harry, Ron, Hermione, Ginny et al would of course play a significant part in the re-building of wizarding society through their future careers.
- Bloomsbury Live Chat (July 30, 2007)
Additionally, as part of the Department of Magical Law Enforcement, Hermione removed “pro-pure-blood” laws.
Katieleigh: Does hermione still continue to do work with SPEW and is life any better for house elves!
J.K. Rowling: Hermione began her post-Hogwarts career at the Department for the Regulation and Control of Magical Creatures where she was instrumental in greatly improving life for house-elves and their ilk. She then moved (despite her jibe to Scrimgeour) to the Dept. of Magical Law Enforcement where she was a progressive voice who ensured the eradication of oppressive, pro-pureblood laws.
- Bloomsbury Live Chat (July 30, 2007)
So, the Ministry did change as a direct result of the war, and several laws were changed as well.