Gillespie, Yorkshire's head coach from 2012 to 2016, described as "really poor" and "disappointing" a letter written by Roger Pugh, the chairman of ECB Yorkshire South Premier League, in his chairman's blog earlier this month describing Rafiq as "discourteous and disrespectful".
The letter, which has since been removed, followed Rafiq's claims that he experienced "institutional racism" while playing for Yorkshire, which left him on the brink of committing suicide.
"I didn't like that letter, seeing that letter, I think that was a personal attack," Gillespie told ESPNcricinfo. "It didn't address the actual issue that Azeem raised. It was like it was almost excusing the issue at hand because Azeem was a difficult character.
"For me I thought the chairman worded his letter very wrongly and I'm convinced on reflection if he had his time again, he wouldn't have written that letter because in my personal opinion that letter was wrong.
"He was almost excusing the issue at hand, this racism issue, because Azeem was a difficult character on the field in some games of cricket."
Gillespie's time at Yorkshire spanned both Rafiq's stints at the club, from 2008-14 and 2016-18, which Gillespie said included some difficult times for Rafiq.
"Azeem has openly admitted, I saw it first hand, there were times when Azeem was a difficult character," Gillespie said. "But racism is a completely different issue to a difficult character, or someone who has done the wrong thing, completely different.
"I just thought it was a disappointing letter, and I think a lot of people would probably think exactly the same as me."
Gillespie said he did not see or hear any racist treatment directed towards Rafiq at Yorkshire. He recalls a moment when he saw that Rafiq, who had been struggling with his bowling at the time, was visibly upset, and offering to help.
"I remember at the time thinking quite specifically that he's obviously really upset about how his cricket is going because he was struggling with his bowling," Gillespie said. "I had no idea he was actually going through other things, and the things that he's actually alluded to.
"I just stood there, put my arm around his shoulders and said, 'mate, if you're not okay, you can tell us, we're here to talk, whatever you need, if you want a coffee, let us know'.
"He's alluded to since then that he was battling some other things as well which he's been very open about but I don't remember anything specific.
"I can only go by what I saw and I saw a young man that was having some battles. I didn't know what all those battles were. I knew that he was really struggling with his bowling but little did I know that all these other things were coming out and I was just doing what I do as a coach and a man manager, I was just there for a player and if he needed my support."
Rafiq has described Gillespie - who led Yorkshire to promotion from Division Two of the County Championship in 2012 and then back-to-back titles in 2014-15 - as "amazing" during his time at the club, and gave similar praise to Joe Root and Paul Farbrace.
Yorkshire have engaged an independent law firm to investigate Rafiq's allegations and appointed a sub-committee including prominent figures in the British-Asian cricket community to review its findings.
Now aged 29 and pursuing a career away from the game, Rafiq became the youngest captain in the club's history when he led Yorkshire in a T20 against Durham in 2012. But his career at Yorkshire came to an end in tragic circumstances when he was released in 2018, shortly after the still-birth of his son.
Gillespie recalled Rafiq as a talented captain before losing his way and then working towards his comeback in 2016.
"His captaincy, his vibrancy, his leadership was excellent," Gillespie said. "He gave great energy into that role and performed it well. Then there were a couple of years he probably just lost his way a little bit.
"He did at times let himself down in and around the group. We discussed that. We ended up releasing him and he had to go and sort himself out, which he did. He went overseas for a little while and his cricket was coming back and we managed to get him back on board, which I thought was a great story in itself after the time he'd had.
"Then I finished up at the club [in 2016] and left and then in the time after I left, things obviously reared up and it was sad for me as a former coach and having been around the group to see that that had happened, obviously disappointing."