How does a fighter “thump” an intercepted aircraft?
'Thumping' is an (unofficial) term for maneuvering the aircraft so that the other (target) aircraft is caught up in its wake. As a practice, it seems quite widespread, atleast during cold war scenarios, and is explained elsewhere:


  Aircrews call it “thumping” — the aviator’s version of a baseball hurler’s brushback pitch. A fighter jet zooms up behind a lumbering reconnaissance craft, then blows past with afterburners blazing, pulling up and away just in front of the larger plane so its jet wash disrupts the airflow around it.


The effect is the same as flying into other aircraft's wake turblence, though the effects may not linger as long as the aircraft passes quite fast (that being the idea- to harass, rather than to cause an accident).

That said, I doubt it was done deliberately in this case as it is quite dangerous to both the aircraft and intercept procedures are quite clearly defined.



Intercept procedure; from FAA media release

Note that it specifically states to be cautious of wake turbulence. Maybe the author got caught in the wake turbulence of the fighter accidentally and it brought back memories of his service days.