Grammatically, it's ambiguous:
Existential psychologists differed from [others often classified as humanistic in their comparatively neutral view of human nature and in their relatively positive assessment of anxiety].
Existential psychologists differed from [others often classified as humanistic] in their comparatively neutral view of human nature and in their relatively positive assessment of anxiety.
So in theory, either is possible.
Practically speaking, reading 1 seems unlikely. The sentence as a whole seems like it's intended to describe "existential psychologists", so reading 2 is more natural. But to be sure, we need additional context or information you didn't include. In context, only reading 2 makes sense; these psychologists embraced existential angst à la Kierkegaard or Sartre.
As for a general rule? Go for what makes sense in context. Isolating complex sentences almost always makes them harder to interpret.