"This story seems to support the narrative that the US intelligence community is actively opposing the executive arm."

I don't think so.  Such calls (like these with Russian officials) appear to be routinely monitored, and this has likely gone on for decades.  This story appears to show that the intelligence community knew that what Flynn said and did was at odds with what he told the government (Pence).  People inside appeared to known this, and nothing had yet been done.  It was the leak to the media that brought this into daylight and let to his resignation.  

It does appear that the leaker was actively undermining the executive office.  There are legimate worries about that, but the biggest concern at this time is who of Trump and his circle knew what what happening and when did they know it?  If they knew and did nothing, that is a huge problem.