A few points:
1. The cherem of the Gra against the chassidim marked perhaps the end of the cherem as an effective punitive tool. Then, and since then, the cherem has been at best ineffective, often a bad joke, and at worst, a chillul hashem.
2. The cherem against the chassidim was a colossal mistake that was unfortunately repeated. Read Wilenski’s “Chassidim U’misnagdim” for proof. It’s two volumes and worth every page.
3. The “way of the Gra” was not the norm in his time. Even the city of Vilna did not accept his minhagim. Today, his minhagim are followed among only select groups, and even that on a pick and choose basis. Yes, even amongst the prushim in Yerushalayim.
4. Comparing the lomdus of the Besht vs. the Gra is as fruitful as comparing the lomdus (l’havdil) of Bach vs. Rembrandt.