a very confusing point for a non-native

First, the original sentence is grammatically incorrect. 'is' is in the present tense. However, 'recently' implies that we're talking about something that happened in the recent past. The correct version would probably use the present perfect tense. This tense is used for things that started or happened in the past, and don't have a clear end point. (If something has been discredited, it hasn't stopped being discredited, so this tense is appropriate here.)

Recently, the Stasist position has not been entirely discounted by new research.

Second, this is an unusual use of the word 'discount'. Usually, if you use 'discount' in this sense, you'd refer to a person's own evaluation of research, like this:

"I discounted the research due to its poor methodology."

You wouldn't really say that the research has been 'discounted by its poor methodology.' It's possible, but 'discredited' would be more appropriate. The GMAT doesn't directly test vocabulary, but I'm bringing up this point because it makes me think that this probably isn't a very well-written problem.

As for your question, if something is not entirely discredited, that usually means that it's been a little discredited, but not completely discredited.

Compare it to these sentences:

Her shirt is not purple. = it could be any color, as long as it isn't purple.
Her shirt is not entirely purple. = it probably has some purple on it (although it might not, depending on the context), but it isn't 100% purple.