Mr Aitken told the Otago Daily Times he was aware of student "high jinks" at the college dating back decades, but had few concerns about alcohol abuse, no reports of drug use and only minor instances of bullying to deal with in his time as master.
However, societal changes meant it was time to put an end to some traditions, such as the bathing of first-year students by older students, he said.
Bathing saw first-year students placed in a outdoor bathtub of water as "good-natured" punishment for breaches of other traditional college rules, or on birthdays, but ended when Mr Aitken had the bath removed in late 2010.
In the past, some unfortunate students have been bathed in water dirtied by other substances, or even shared their baths with eels, the ODT has been told.
However, Mr Aitken said he emphasised the need for only clean water to be used in his time as master.
Even then, the risk of unintentional injury or health problems meant he decided to end the practice by having the bath removed.
"Over the last few years . . . health and safety issues have become prominent and society has changed, and it was time to do away with those traditions.
"Potentially, it was a dangerous activity, so that's why we got rid of it."
The end of the bathing tradition had been followed by the closure of the Buttery bar inside the college last year.
And, last week, the ODT reported the Presbyterian Church had replaced the college's master and council with a commission of the church's general assembly.
The commission had also moved to ban initiation ceremonies, scrap elitist symbols and tighten rules governing alcohol at the college, after a seven-year review which found alcohol had "been a concern" at the college.
Mr Aitken rejected any suggestion alcohol use by college students was out of control, saying many residents either did not drink, or did so only moderately, while "one or two clowns" had been dealt with.
"I had few concerns about that at all. Naturally, there would have been one or two students from time to time who I suppose were a little the worse for wear, but they were always dealt with properly, and ... if necessary punished in an appropriate way."
However, the alcohol changes aimed to bring the college into line with the rest of society, and changes expected with the review of New Zealand liquor laws, he said.
Past and present students concerned by the changes voiced their opposition on Facebook, with many accepting alcohol rules had to change but fearing other treasured traditions were being lost amid the shake-up.
That included a ban on "feather-ruffling" initiation ceremonies for new arrivals, as well as the use of the term "fresher" to describe new students.
Traditional names for the Buttery, Porters Lodge and Ab Epistulis were also changed, and would instead be known simply as the canteen, reception and administration officer.
A requirement for semi-formal dining attire at Knox was also dropped, and the Knox College Students' Club had lost control of its budget.
A smaller number of former students supported the changes, with one - writing on the ODT website - comparing old rituals aimed at first-year students to "hazing-style initiations", while another said the changes were long overdue.
"Knox has some great cultural traditions but has lost the plot. A fresh start is well overdue.
"The culture of drinking [as bad as any at Otago] and organised stupidity, thinly disguised as tradition, is no longer acceptable, if it ever was."
Mr Aitken said yesterday it would be "inappropriate" for him to comment on whether he supported the commission's changes, as they had been introduced after his leave began.
He also declined to explain exactly why he was on leave, except that it was "appropriate" while the commission worked and his absence was not performance-related.
Asked whether he expected to return as master, and if so when, he replied: "We will have to see.
"I have no idea. It is a wee bit like limbo."
