Andrew - the Associate Congregation churches were breakaways from the COS as you surmised and the history of the Erskine Church in Falkirk paralleled the changes in Perth. In most congregations there was a subsequent further upheaval when the Free Church was formed and in some cases even further schisms. The current situation is a bit confused. Some congregations moved en masse into one or other camp, others sub-divided, some retaining the name but not the building, others changing their name to make clear their allegiance. At one stage Perth had 6 'Free' churches. What the present state of your ancestor's church would be I couldn't say.