I can't imagine why in Chabad, where mesira from misnagdim led to prison and death sentences starting from the Alter Rebbe on down, wouldn't see the hisnagdus as something that contributed positively to chassidus.
I guess it will have to stay a Machlokes between Dan and the Apter Rav.
On a more serious note, you are right that the hisnagdus was more painful to Chabad than to other places, but pain does not mean non-beneficial. The Apter Rav, and perhaps the Tzemach Tzedek, believed that there was something positive to it, Chassidus benefited from it.
Personally, I feel that the interconnectedness of Klal Yisroel means that all gain from each other, and that is something to be proud of. I cannot imagine a world of Galicaner Poskim without a Sefardishe Maharit, or Litvishe Gedolim without a Shulchan Aruch Harav, or anyone without an Italian Mesilas Yesharim. We all need each other.