It was one of those moments in which what was not said appeared far more interesting than what was. Stewart Regan, the chief executive of the Scottish Football Association, on Friday refused to discuss whether his recommendations were fully implemented by the governing body's refereeing committee regarding the messy affair surrounding Dougie McDonald. It was hardly difficult to infer that Regan, who has only been in his post for a matter of weeks, had for the first time encountered the sort of obstruction for which the SFA are widely criticised.

The issue itself surrounding McDonald is trivial, but context is everything. The implications of what occurred during a game at Tannadice earlier this month, added to the lame "punishment" handed down by that committee, will be far-reaching.

In reversing his decision to award Celtic a penalty during their match against Dundee United, McDonald was correct. His flawed move to implicate the assistant Steven Craven, nonetheless, both during the game and in subsequent discussions with the SFA's refereeing observer remains a dubious business. And a damaging one for the reputation of Scotland's refereeing fraternity. A genuine copy of that observer's report has even been plastered over internet forums.

Regan's explanation of events, namely that McDonald didn't want Craven to take part-responsibility for the initial and wrong award of a penalty, makes little sense. Craven, who has resigned from refereeing, is due to explain his anger in a tabloid newspaper any time now. Hugh Dallas, the SFA's head of refereeing, may well come under deep scrutiny having repeated McDonald's initial and incorrect story in public.

In any other walk of life, McDonald would feel the full wrath of a human resources department for essentially landing a fellow employee in it. Despite Regan's claims, that appears to have been as a means to protect McDonald himself, not Craven.

As McDonald awoke yesterday morning to a headline that screamed "I Lied", he could take solace from the fact things could and possibly should have been worse. The 45-year-old's career in officialdom was at stake within the last week.

For the make-up of the committee, to which Regan reported the findings of his investigation into the Dundee events, highlights one of many obvious flaws within the SFA. Its refereeing committee comprises six former referees out of a seven-man panel. This is the equivalent of the players' union presiding over disciplinary matters relating to their own members in the Scottish Premier League.

Clubs, particularly at a lower level within the Scottish game, will not need reminding of the SFA's fierce penal approach – often in monetary terms – if administrative errors are made.

Celtic will seize upon the SFA's leniency towards one of their most prominent referees. McDonald has merely been warned for bending the truth during conversations with his superiors and will continue to official in Scotland's top flight. The Parkhead club have stepped up their campaign for clarification from the SFA over what they perceive are a host of incorrect decisions awarded against them in recent times.

If such issues are subjective in part, the proof that the SFA is willing to go easy on a referee found guilty of being economical with the truth is cut and dried; there has been a clemency displayed that leaves onlookers to wonder on what other matters officials can collude with each passing game. The relationship between the outside world and Scottish referees, already at an all-time low, will continue to deteriorate.

McDonald's position now is hardly enviable. The Edinburgh-based official cannot take charge of a Celtic game in the near future without allegations being thrown his way, either for supposed bias towards or against that club. Such hubris would cause an unnecessary sideshow for the match in question, but is inevitable.

Regan, meanwhile, will face further calls for increased transparency and accountability relating to referees. Those are seldom backed up by examples of what improvements can be made, yet the McDonald affair proves one thing; Scottish referees will continue to lead charmed lives when their judge and jury are from the same background as themselves.