BH doesn't really have a "business" per se other than being a holding company. BH already owned an incredibly diverse portfolio of companies before acquiring BNSF, from See's Candy to GEICO. BH originally, before Buffett, was textile manufacturing company. Buffett went heavily into insurance, then into anything that was profitable, undervalued and well-managed in Buffett's and Munger's analysis.
Buffet's approach has always been to let the existing management run the company, stand back, and leave it alone. Part of their acquistion strategy is that they evaluate the management in place and consider that management part of the assets they are buying. I know BNSF's management was left in place. BH itself has a tiny, tiny staff, deliberately, and really doesn't have the capacity or the desire to dig in and closely run any of it's acquired companies. It doesn't have very many "suits".
So this talk about BH interfering with BNSF isn't consistent with Warren Buffett's MO. Not to say it isn't true, I know no details here, but it is certainly inconsistent with Buffett's philosphy and track record and makes me wonder about that theory.