There is a difference between keeping Torah in truth and the false appearance of Torah of the religious world. Not that this always was the case. But that was the point of the signature of the Gra on the letter of excommunication.  That is to make this difference clear.

The result of his signature being universally  ignored created the situation that the Sitra Achra [Dark Side] got inside and took over the religious world.

[However I think that Rav Nahman was not included in the excommunication since one day I was walking around the old city of Jerusalem and happened into a small library that had the very famous book that printed all the different letters of excommunication plus and the word for word testimonies that were collected in Vilna. So I saw the actual wording if the letter that the Gra signed. Rav Nahman  would not have come under that heading. See for yourself if you are interested.]

At any rate, the actual result is that in order to keep Torah one has to run away from the religious as far as possible,