I get what you're talking about; it's called linguistic relativity (sometimes referred to as the Sapir-Worf hypothesis). But it's not as strong of an influence as we might think. Most of the research, from my limited understanding, suggests some weak but non-trivial ways this shows up.

For example, this study deals with concepts of (relative) space and how they may influence or reflect the underlying cognitive thinking.

A close look at the linguistic development of children raised in Dutch-, English-, Tzotzil-, and Korean-speaking homes shows that children do not start from a common conceptual core, given say by innate presumption or biological endowment, but from the earliest point of language production already make distinctions more like adult speakers of their own languages.

[...]

As Bowerman (9:170) concluded with respect to the production evidence, “there was little evidence that [the children] had strong prelinguistic biases for classifying space differently from the way introduced by their language. This leaves the door open to the possibility that, after all, spatial thought—undeniably one of our most basic cognitive capacities—bears the imprint of language.”

It's fascinating stuff. I will say that I myself have noticed some interesting quirks of the languages I've studied that kind of coincide with various stereotypes about those cultures, but it's hard to go farther than that. For example, have you ever wondered whether Russian's rather oblique way of talking about possession has some connection to the way Russian society views ownership or individualism? Or is it a reflection of that, or totally unrelated?

Meanwhile, I've wondered if the reason the Greeks were so good at philosophizing is that Ancient Greek is extremely good at abstractions, and tends towards really broad meanings in words. I don't speak Latin, but one of my Greek professors (who speaks both) told us once that reading philosophers in Latin you could often see them struggling to get their point across because Latin just doesn't lend itself to abstract concepts the way Greek does. I don't know how true that is, and again I don't know in which direction the causation runs (if it exists at all). But it's fun to think about.

Turning back to your examples from Esperanto, I think it's all in how you approach it. For me, I don't really think about the mal- prefix as being anything other than "not," and have never thought about it as having any moral connotations (especially since there are other affixes that do suggest either "badness" (aĉ)- or mistake (mis-).