For MacKay, his political career had come to a standstill. By making a deal with Harper to bring the PC Party into the Reform fold, he ensured his position as a power broker within the party and caucus. But it also limited his opportunities to become Leader and PM. That would only have happened if the CPC suffered a significant electoral defeat, or a internal party coup took place. With the former, the party wouldn't recover and he would not get to sit as PM. And with the latter, Harper's tight grip on the reins and micromanaging every aspect of the government apparatus, a regime change was not likely to happen.
I believe that MacKay does want to step back from public life for at least the near future. Even Solomon makes a good point about MacKay's own experience as a child of a political power broker:
http://www.cbc.ca/news/politics/timing-of-peter-mackay-s-departure-politically-damaging-1.3093969
MacKay has a young family and he and his wife are expecting a daughter in the fall, so his explanation that he wants to spend time with his young family is understandable. His own parents divorced when he was young, and his father Elmer, a minister in the Mulroney cabinet, was often absent as MacKay grew up. It is an experience he has publicly said he does not want to repeat for his own children.
But what raises a big question is the timing of the decision, not so much because it throws the election strategy into chaos, but rather MacKay filed the nomination papers, and told the press in February that he was ready for the upcoming campaign. And with the departure of other high profile members, Harper made it clear that anyone who was planning on not running this fall had to make their intentions known so plans could be made, and the announcements managed.
What changed in the interceding 3 months?
And as some of the pundits have pointed out, do not rule out an eventual return to political life.
https://youtu.be/UPw-3e_pzqU