There will be some frank conversations when Pat Howard next speaks with the Test squad, most likely in Darwin during the training camp that starts next week.
Smith said Warner has nothing to fear regarding potential retribution from Howard and Cricket Australia (CA) chief James Sutherland.
"No, I think he'll be OK," Smith told Fox Sports.
"Obviously he's been very vocal and he's supported the ACA through this whole thing and he's been great.
"Some guys have been really vocal on social media."
Smith added he had to be "careful" given his working relationship with both CA and ACA officials.
"The way for me to lead in this dispute is to be able to talk to the guys behind the scenes, who are important and who are at the table," he said.
"And try and get this dispute solved as well as I can.
"It's had some difficult moments ... I've been talking to both (ACA boss) Alistair (Nicholson) and Pat Howard on the phone most days. It's been a long process."
Pay talks between CA and the ACA continued into Tuesday night, with Smith noting "there's a few things to finalise and tick off" before an agreement can be signed.
Warner isn't the only star to result in raised eyebrows among CA's bigwigs.
However, the relationship between unemployed players and administrators has strained on several fronts throughout the saga.
Many players remain disappointed with CA's hardline approach throughout the scrap, especially Sutherland's refusal to involve himself in talks during the first half of the year.
Michael Clarke and Mitchell Johnson both opined recently it will take some time for trust to be restored.
"If there's been any damage it can be repaired," Smith said.
"There's obviously been some arguments amid trying to get a resolution.
"We're just looking forward to it coming to a close and getting out there and playing some cricket."
- AAP