As any good author, Claremont tried to understand Magneto's motivations, to make them logical.
Once, you understand someone's motivations, it is less easy to hate him.
But, in Claremont's world, a villain stays a villain even if you can understand him. So, no, Claremont's Magneto was never shady: there were more relationships between Magneto and the X-men when Magneto became more and more reputable.
At no time, the X-men compromised their values on behalf of the 'mutant cause', back then.
“Strength is the lot of but a few privileged men; but austere perseverance, harsh and continuous, may be employed by the smallest of us and rarely fails of its purpose, for its silent power grows irresistibly greater with time.” Goethe
Read Fantastic Four, they've got various classic runs. They built the Marvel universe as we know it today. Black Panther, the Inhumans, Galactus, Silver Surfer, the Watcher, Annihilus, the Kree, the Skrulls, Doom, Adam Warlock, and the Negative Zone all come from their comics.