The Bombers' board will speak to Hird next week before making any decision on his future after Hird's wife Tania this week revived claims AFL CEO Andrew Demetriou tipped-off the Bombers about the supplements scandal.
After launching his second stint as a senior coach with an impressive 39-point win over North Melbourne on Friday night, Thompson said his relationship with Hird had not soured.
However, he said the Bombers needed to be careful how they handled the supplements scandal in 2014.
"One of the things we don't want to do is embarrass the AFL, the game, our supporters," Thompson told 3AW on Saturday.
"We just want to get through this year and deal with what we're dealing with.
"I find the best thing is for me to do my job and for 'Hirdy' to let me do it.
"Hopefully he trusts me that I'm going to look after his team.
"I have a lot of respect for the man, totally, and the situation is what it is and we're dealing with it."
Thompson said he would talk to Hird at points this season but the pair would not have a weekly catch up after games.
"I think he's in this period where he's doing school work for 12 hours a day, so I'll talk to him periodically, but nothing on a routine basis," he said.
Hird is in Singapore as part of a study tour and could not be contacted by Essendon chairman Paul Little on Friday.
Speaking ahead of Friday night's match, Little described Tania Hird's comments, made in an interview on 7.30 on the ABC, as "inappropriate".
"We really want to speak to James, what he knew and what was motivating Tania," Little told 3AW.
"Because we haven't been able to speak to either of them at this point in time, we are putting that off to next week."
Twitter: @AFL_Nathan
