Although MK hasn't been a full time Bethesda employee since 2000, he has consistently been doing work for them as an independent contractor ever since. He has been hugely important in shaping the series. Some even go as far as to say that without Kirkbride, the Elder Scrolls would just be another typical Tolkein-fantasy borefest. All of the most important religious texts in the series were written by him:
The 36 Lessons of Vivec,
The Commentaries on the Mysterium Xarxes,
The Song of Pelinal, and the
Nu-Mantia Intercept (most of which later became part of the
Book of the Dragonborn). Bethesda even uses material that he creates on his own time. Heimksr quotes passages from
From The Many Headed Talos verbatim.
The Seven Fights of the Aldudagga and
The Five Hundred Mighty Companions or Thereabouts of Ysgramor the Returned are responsible for a lot of lore elements in Skyrim, including Whiterun's Companions and the culture of giants.
There's no debate regarding whether or not Bethesda endorses MK's work. The controversy arises from ES fans who can't stomach his more outlandish works - particularly the science fiction.
Loveletter From the 5th Era and C0DA, for example. Both can be read
here. Some people think that this sort of thing has no place in muh dungeons and dragons. Joke's on them, though. The Elder Scrolls has been sci-fi fantasy ever since work began on Morrowind.