Unlike most members of the Church of Scotland, Haliburton supported episcopacy, and was an active persecutor of the Quakers.
Haliburton moved to Newtyle parish in Angus, assisting the work of an episcopal minister there until the Church of Scotland forcibly took over control of it in 1698.
Haliburton became increasingly sympathetic towards Jacobitism and ordained clergy, working closely with re-established episcopalian bishops and archbishops, though the latter often did not inform him about the secret consecrations of new bishops which were taking place.
Twenty days earlier he had attended the raising of the standard of the Old Pretender at Fetteresso, the act which initiated the First Jacobite rising.
He married Agnes Campbell of Keithock widow of David Haliburton of Pitcur (a cousin).