Dr Conroy was previously director of religious education and pastoral care at St Andrew's College, Bearsden, and his elevation will be seen as a signal that the training of Catholic teachers is safe in the university's hands.
But the appointment has attracted criticism, within and outwith the faculty, from those who favoured the other candidate in a "two horse" race, Professor Jean Barr, head of the university's department of adult and continuing education.
The contest pitted an academic, whose specialism is religious and moral education and whose most recent publications have been on Catholic and values education, against another whose research has focused on adult education and feminism.
The polarisation between their academic interests will be seen as epitomising the conflicts which existed between the two camps following the merger of St Andrew's College and the university's education department.
The merger was scrutinised by the Scottish Higher Education Funding Council which acknowledged the unease and tensions in joining a research-led group of academics with another cohort specialising in Catholic teacher training.
Hirek Kwiatkowski's four-year tenure as the present dean is seen as having gone a long way to stabilising the faculty.
Eric Wilkinson, deputy dean of education, who voiced early concerns about the role of the Catholic Church in the running and direction of the faculty, said: "The frenzy that was around has certainly diminished considerably. There is much more evidence of collaboration, less suspicion and there is more security in people being able to maintain some sense of identity."
But Stephen Baron, a former member of Glasgow's education faculty who is now with Strathclyde University, criticised Dr Conroy's appointment: "Any disinterested observer would not be able to understand the preference for Jim Conroy over such an eminent academic as Jean Barr without understanding the denominational issue that lies behind it."
However, Dr Kwiatkowski, who will remain dean until August, said: "As far as the other candidate is concerned, I would not want to take claims about Professor Barr's superior research credentials to a court of law. They are different, but they both have credibility and the appointing committee was very aware of what I suggested they had to look at."
Professor Baron warned that the future of the Glasgow faculty depends on its research performance, "which currently is declining terribly". It suffered a setback when it failed to win the lucrative contract for the Government's applied educational research scheme (AERS), of which Professor Baron is the co-ordinator.
While the main players - Strathclyde, Edinburgh and Stirling universities - formed a consortium, Glasgow backed a separate, ultimately unsuccessful, bid from the Scottish Council for Research in Education, which is now housed within the faculty.
Exclusion from the AERS programme has left Glasgow with less access to research funding and more isolated from collaboration opportunities. The faculty recently called in Professor Sally Brown, who was the chair of the education panel for the last research assessment exercise in 2001, to evaluate its research position for the next round in 2008.
It won a rating of four last time, the same as the faculties at Strathclyde, Edinburgh and Stirling. Professor Brown says Glasgow will have to work hard to maintain its position in research terms - and any drop in the ratings will impact on its funding and status.
Professor Wilkinson accepted that "we have an uphill struggle" and that the new dean "must provide clear leadership for our research agenda". Dr Kwiatkowski said the faculty would be trying to double the number of staff submitting their work to the next research assessment exercise.