Pulis managed the Gills between 1995 and 1999, guiding the club to the brink of the Championship before leaving in acrimonious circumstances, which ended in a court case.
But Scally's instistence that he could never forgive Pulis appeared to leave him in a minority of one as the Potters boss received a standing ovation from the Gillingham supporters.
Both sets of fans were cheering his name at the end of a game in which Gillingham took a deserved lead through Danny Kedwell before Stoke ran out comfortable winners.
"If he (Scally) wants to say stuff, it's a free world. He can say what he wants. You've seen who really counts and that's the supporters," Pulis said.
"I have been a manager a long time and I have never had all four sides of the ground stand up and applaud me when I walk on the pitch, and singing my name at the end.
"It was fantastic. That is what you work for at a football club - the supporters and the people in the area.
"I had a great four years at the club. I can remember my first game here against Wigan in front of about 2,300 people.
"My last game was at Wembley (in the League One play-off final) and we took 38,000 there.
"It has put me in good stead. It made me a better manager. In four years I was able to build a football club that I thought could push on, and did push on.
"That reception will stay with me for a long time. It was very, very special. I didn't realise it was going to happen.
"It has been 12 years since I left the football club. So to be held in that esteem after 12 years - there aren't many managers who get that."
Despite the fans' clear support, Scally banned Pulis from all areas of the Priestfield Stadium apart from the dugout, the tunnel and the away changing room.
Pulis was not even allowed to enter the press conference room.
"That has happened the three other occasions I've been here, so it's nothing different," Pulis said.
"It's the way it is, and I never go upstairs for a drink, even when we play at the Britannia. I never go in the boardroom afterwards - I'm not a boardroom man and I have never done it in my life. So it makes no difference to me."
Gillingham made a bright start and led after 16 minutes with a goal from Kedwell, who later went off with a cracked rib to increase the already-pressing need for manager Andy Hessenthaler to strengthen his resources up front.
Stoke responded with goals from Jon Walters, Cameron Jerome and Robert Huth in a 15-minute period around half-time to ultimately reach the fourth round with ease.
"When it came out of the hat it was a draw you thought was set up for it [an upset]," Pulis said.
"I thought we started really slow and couldn't get into the game. When they scored you think 'blimey, let's hope we're not on the end of one'.
"But from that point we gradually took over."
Gillingham put in a spirited effort and continued to cause Stoke problems even after falling 3-1 down, with Swindon target Luke Rooney particularly effective off the bench.
Swindon, who caused the biggest upset of third round by knocking out Barclays Premier League side Wigan, revealed this week they had lodged a "six-figure" bid for Rooney - much to Hessenthaler's anger.
"I am not going to get into a war with Swindon but to put that into the press a day before a big FA Cup tie, I am disappointed in their chairman and I know my chairman is livid as well," Hessenthaler said.
"They had a private conversation and to go out on Radio Wiltshire and say they have made a six-figure bid, it is not good conduct. That is how we feel."
Hessenthaler's desire to make Jo Kuffour's loan move from Bristol Rovers a permanent one increased after Kedwell went off injured.
"It is going to be a concern to us and something we need to deal with over the next couple of days," Hessenthaler said.
"Now that Kedwell is probably missing, the chairman and I have a bit of work to do over the next couple of days to maybe bring in some new faces.
"We want Jo to come and if we can bring another body in that would be nice."