Does "so called" have a negative connotation in English?

It's true that OED's first definition for so-called is just called or designated by that name, but the most recent citation for that "neutral" sense is 1863. So even though OED don't explicitly identify it as dated/out-of-fashion, that's what I would say. The "current" definition is...

Called or designated by this name or term, but not properly entitled to it or correctly described by it. Also loosely or catachrestically as a term of abuse.

It's particularly worth noting their most recent citation for that sense...

1980 W. Safire in N.Y. Times Mag. 13 Jan. 6/1
Examples of sneer words are ‘self-proclaimed’, ‘would-be’, ‘purported’ and that Soviet favorite, ‘so-called’.

If William Safire says it's a sneer word, that's good enough for me.

Turning to OP's first example, I would say that the "translation" is inherently flawed, since no negative connotations are intended. Depending on context (primarily, the target readership), it might be better rendered as...

1: The government approved exceptions for "non-pedagogical" (non-teaching) workers.
2: The government approved exceptions for workers classified as "non-pedagogical".

Or you could simply omit so-called and leave it at that, for a "neutral" reference. The use of "scare quotes" doesn't necessarily carry negative connotations, so it's a credible way of simply introducing an unfamiliar technical term or usage without it being value-laden.

EDIT: In light of the many respondents supporting so-called inaffectionate ¹ use of the expression, I think it's only fair to point out that Google Books claims 1650 instances of "so-called quanta". It's simply not conceivable any of them would be denigrating either the term itself, or its use in the context of some referent undeserving of the label.

In reality there are only 23 instances (of which barely a dozen are visible in context, and within that most are duplicates), and they tend to be older. But it can't be denied that some people still use the term neutrally. So we must be prepared to admit of that possibility if ever we come across a "perplexing" usage.

¹ This is from subscriber-only OED - I can't find an online definition of the usage...
inaffectionate, adj. Obs. rare. Unbiased, unprejudiced.

Sometimes it is negative, sometimes not.

Generally if it precedes a term that is familiar and not a proper noun, it is being used to undermine that term. e.g.

Band X have just released their so-called "Greatest Hits" album.

The implication is that the songs on the album are only called "Greatest Hits", but aren't actually great or hits.

Alternatively, it can be simply used to indicate that a category name is really only defined by the things to which people apply that term. For example, from http://www.british60scinema.net/british-new-wave/

Set out in this fashion, a number of things become a bit clearer. Firstly, all the so-called New Wave films have literary antecedents, ...

Here the author is not mocking the categorisation of films as "New Wave", but highlighting that a "New Wave film" is only defined by what gets called a "New Wave film."

It has an opposing connotation.

If someone is bothering to include "so-called" in a phrase, then they are seeing some reason to distance their own claim from that they mention. There's a few different reasons why one might do so, and if the claim is a positive one, then questioning it is negative.

Conversely, if the claim is a negative one, then the questioning it is a positive. E.g. if I describe someone as "a so-called 'criminal'" I'm suggesting that they are not really a criminal at all.

There are other reasons for using the phrase again though. I might just think a wording is stupid, as with so-called "cloud computing".

Of course, one could use it to point out a stupid wording and to cast aspersions on the applied claims, as with so-called "genius bars".