As we all know, there was lots of controversy on this topic within Ahmadiyya.  Further, MGA barely wrote anything..his ghost writers wrote everything, hence the contradictions.  In this case, we have new evidence, and translations from Mujadid-e-Azim, which is mostly in Urdu and hence hidden from the educated parts of the world.  Nonetheless, take a look at these essays:

Also see here:

New Quotes
 “Once Hazrat Mirza asked Shaikh Qamar-ud-Din of Jhelum to show him the verses of the Quran from which the Shaikh had concluded that Jesus had a father. At first, the Shaikh sahib, out of respect for Hazrat Mirza, remained silent. But upon Hazrat Mirza repeating the question, he mentioned the arguments from the Quran that he knew. Hearing the arguments, Hazrat Mirza said: ‘Your arguments are certainly strong, but until God gives me to understand this point, I will follow the views of the majority of Muslims’. … Hazrat Mirza said to Hakim Fazal Din [who had complained about Shaikh sahib’s belief]: ‘How can you declare as heretic someone who bases his arguments on the Quran?’” (Mujaddid e Azam Vol.2 Pg.1342).

”Molvi Nooruddin held the same belief and he once told me that ‘The only reason I stay silent about this issue is because MGA believes otherwise.’  (Footnote) But after the death of MGA, Molvi Nooruddin became the Khalifa and he specifically instructed Molvi Muhammad Ali to write that Jesus had a father in his English commentary of the Qur’an” (Mujaddid e Azam Vol.2 Pg.1342).  

The scans