That's quite plausible, but i am not sure how much flying would a sitting Air Chief do himself, as there is a lot of other work to do as well. I am of the opinion that it had to do something with Musharraf saga, as with Mushaf Ali Mir. From what i have heard, Mushaf Ali Mir sahib once raised his voice at Musharraf (when PAF was looking for western equipment, but Musharraf wanted Chinese), and Musharraf didn't like that. Something similar might have happened in Shahid Lateef case as well.
Rao Qamar Suleman wasn't fit as well as we read recently in the news, when he left his new job at PIA. So we will never know. However, if you listen to Shahid Lateef sahib talking on tv, you can feel some genuine animosity in his speaking style, something one would have when they are not given the expected outcome (in his case, the Air Chief post)