Pulis then suggested the goalkeeper's head had been "turned" by reported interest from champions Chelsea.
Holloway is Godfather to Pulis's son Anthony, but sentiment will count for nothing on Sunday.
Pulis also disputed the decisions that led to Faye's red card on 87 minutes.
But Iwelumo's looping header on 88 minutes snatched an unlikely point for Tony Pulis' men.
But despite his bitter departure, Pulis is relishing a return to the Kent club.
"Gary's a decent person and I'm disappointed for him, but that's the way football goes, " added Pulis.
Neither Bristol City's Gary Johnson nor Stoke's Tony Pulis started the season anticipating a sustained promotion challenge.
Pulis is in his second spell at Stoke, having returned to the Britannia Stadium in June 2006.
And Pulis told BBC Radio 5 Live that he was no stranger to dealing with flare-ups between players.
"He trained on Tuesday, hurt his knee, had an injection and didn't train Wednesday or Thursday, " added Pulis.
But Pulis was adamant the former England striker would be in contention for selection if he is fit.
"Once the whistle goes, we will be in our two corners fighting for the three points, " said Pulis.
Pulis's diligence in researching the transfer market has paid spectacular dividends, with his team second in the Championship.
"The club now is unrecognisable from when I took over for the first spell, " Pulis told BBC Sport.
Such was his form, Etherington was tipped for a call-up to the England squad by Stoke manager Tony Pulis.
"We have moved on and everything is well now, " the 23-year-old Begovic, who denied Pulis's claims, told BBC Sport.
"It's easy for referees to make decisions like that against clubs who are maybe not as big, " said Pulis.
"He has always wanted to play in Germany and missed out on several occasions in the past, " Pulis added.
But Pulis said the story should never have emerged in the first place.
Stoke boss Tony Pulis said he had helped Tuncay achieve his "dream" move.
Holloway and Stoke boss Tony Pulis are firm friends who met while on the playing staff at Bristol Rovers.
When Pulis returned, the Icelandic contingent that ran the club had left and Peter Coates was back as chairman.
"We gifted them three very, very poor goals, " Pulis told BBC Radio Stoke.
BBC: Stoke striker Kenwyne Jones pleased to end goal drought
Stoke were 1-0 down at St James' Park when Pulis brought Fuller on for Glenn Whelan just after half-time.
But after a slow start Pulis' men edged their way into the match.
Stoke manager Tony Pulis conceded his team were beaten by a superior side.
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"It's something we have to look at, " added Pulis, who believed there should be official time-keepers as in rugby league.
Stoke boss Tony Pulis has already said that they may make a fresh bid for the 22-year-old, a long-term target.
He left his role as coach of the Thailand national team to become assistant to Pulis at the Britannia Stadium.
It left Pulis with a significant problem as he set about building a new squad, with the difficulties that involves.
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