I've always found that outlook interesting.
The Spirit Cats, with their focus on mysticism and spirituality, stayed truer to their Nova Cat roots than the main body of the Nova Cats. Reading the material, you see a loss of faith amongst the Nova Cats in the Combine, and yet they're held up as the epitome of the Clan. The Nova Cats in the Republic are viewed positively because they're good little house cats that stay in their enclaves and give all their technological secrets to the Republic.
The Spirit Cats are demonized, marginalized and viewed as dangerous 'cultists' because they followed the vision of a leader, a vision that led them to betray their patron society, the Republic. But the main body of the Nova Cats did that twice before: when they broke with the Clans to join the Star League, and when they ran off to join Stone's Coalition (aka. the Republic).