So does that mean they married in Church of Scotland and not RC Church?
Not necessarily.
The wedding probably didn't take place in a church building at all. It was customary for the wedding to be held in the bride's parents' home or, if she had no parents or was married a long way from home, in her employer's home or in the parish manse.
Officially the Church of Scotland was supposed to keep a record of all baptisms and marriages irrespective of the participants' actual denomination or the variety of clergyman who performed the ceremony.
In practice, this didn't happen. In some parishes the clerk didn't even manage to keep a proper record of the baptisms and marriage in the C of S, never mind other churches. Especially in populous urban parishes or very large rural parishes, the clerk usually wouldn't know about baptisms or marriages of RCs, or Episcopalians, Congregationals, Baptists, or parishioners of other dissenting denominations or non-Christian religions unless they came and told him.
185 years after the event, and in New Monkland, it's not going to be possible to find out from the records exactly where the wedding was held or which clergyman officiated.
As for disparity in records, if Ancestry (or MyHeritage, or FamilySearch, or FindMyPast, some other commercial web site) says one thing and the original document at Scotland's People says something different, go for the original. Your 'hint' could be a mistranscription of the original, or a guess or assumption by someone who hasn't found the original, or a figment of someone's imagination.
See also
https://www.rootschat.com/forum/index.php?topic=714261.0