Prof David Fielding told the court he did not think the relationship was appropriate given that Weatherston was lecturing and tutoring subjects Sophie was studying.
But the accused had not broken any university rules.
One of his concerns was the large age difference and the potential for conflict of interest.
But steps were taken so the accused was no longer in charge of the particular course.
Another staff member took over supervision and Weatherston was not involved in marking the papers but he still took the lectures.
Towards the end of 2007, Robert Alexander, Sophie's dissertation supervisor and the internal assessor of Weatherston's thesis, expressed his concerns about the relationship.
Dr Alexander had got to know Sophie quite well and, from things she had told him, he was very worried about the way the relationship was going.
Prof Fielding said he was aware of Weatherston's application for a lecturing position.
He knew of two staff members who supported the application but others who were less enthusiastic - "particularly those of us from overseas" - who had read his thesis or were aware of the quality of work elsewhere.
As to the accused's chances, Prof Fielding said he would not have thought he was "a front-runner" but because it was never certain the best candidate would accept the position if offered, he thought Weatherston was still "in with a chance".
Weatherston was very confident about his work and was slow to make advised changes, although he would make them eventually when he saw it was in his interest.
He was very ambitious, wanted to succeed as an academic and wanted be a lecturer.
Prof Fielding said he had read Weatherston's thesis and thought Dr Alexander's comments were quite reasonable.
It appeared the accused had not given himself enough time and there was a lot of repetition and the presentation was "quite shoddy".
He knew Weatherston wanted to graduate in December and the fact Dr Alexander received the thesis back on October 15 after the recommended changes had been made meant the final reading and assessment was "a tight squeeze".
Cross-examined by defence counsel Greg King, Prof Fielding agreed Weatherston had 24 A-plus marks and one A in his 25 grades.
And he was aware the accused had previously worked for Treasury for a couple of years.
But Weatherston had not "done himself any favours" by his allegations about not being credited for his input into a research paper.
The ability to get on with people would be something taken into consideration if there were candidates with similar qualifications, Prof Fielding said.
He agreed he was aware Dr Alexander did not get on with the accused and was against his being appointed, but he had already had to step down from the selection panel because one of his former students was a candidate.
Prof Fielding also agreed he knew Dr Alexander had pulled up Weatherston's profile and discussed him with Miss Elliott, joking about whether he was wearing make-up in his photograph and whether he was gay.
He agreed it was not a good thing for a staff member to involve students in that sort of mockery.
