Morgan's England play Warner and Smith's Australia at Lord's on Tuesday in the first international game between the sides since the Australian pair returned to cricket following a suspension for their role in the ball-tampering scandal of March 2018.
While Morgan did not call on spectators to show their disapproval for the actions of the Australia pair, he also spurned an opportunity to discourage the boos that have greeted Smith and Warner at some grounds. Virat Kohli, by contrast, had gestured to the crowd to stop jeering and applaud Smith during India's World Cup match against Australia.
"Spectators pay a lot of money," Morgan said. "They can do what they want. You don't know how sports fans will react. Just because two guys have been punished, served their punishment and returned to play, it doesn't mean they will be accepted back into the cricket community straight away. It will take time.
"I'm not expecting anything. I think fans and supporters up and down the country will have different reactions. As they will around the world. So we'll see."
The two men, who were suspended for 12-month periods by Cricket Australia following the incident during the Newlands Test last year, were booed by some sections of the crowd when England and Australia played a World Cup warm-up game in Southampton in May. There was little sign of it discomforting Smith, who made a match-winning century.
"Just because two guys have been punished, served their punishment and returned to play, it doesn't mean they will be accepted back into the cricket community straight away. It will take time" Eoin Morgan
The Lord's crowd tends to be a little more genteel than most and booing here is unusual. But the World Cup may appeal to a different demographic to 'normal' matches at the ground and a spokesperson for the MCC - the ground's owners - told ESPNcricinfo that "personal abuse will not be tolerated" but stewards would be briefed to help differentiate "between abuse and banter". They also reiterated that fancy dress is not permitted at Lord's and that, for security reasons, a bag search will be in operation. Whether this includes the confiscation of strips of sandpaper remains unclear.
Aaron Finch, the Australia captain, insisted "it won't make any difference" if the crowd boos and suggested it might even provide his players with "more motivation".
"As a player you don't tend to hear what people say," he said. "You hear the noise at times but not the specifics and I'm sure it will be the last thing on Steve or Davey's mind when they walk out to bat. If a handful of people or the whole stadium is booing, it won't make any difference to how hard they're watching the ball or anything like that. It's just a bit of white noise.
"It hasn't affected our boys one bit, I can honestly say that. If anything it has given them a bit more motivation."
Morgan's comments follow similar sentiments from Jonny Bairstow. Bairstow, who experienced some interesting times on the last Ashes tour, made reference to former Australia coach, Darren Lehmann, calling on home supporters to "give it to him [Stuart Broad] right from the word go for the whole summer" in the "hope he cried and he goes home" ahead of the 2013-14 tour.
"There was a time not that long ago when the then Australia coach, Darren Lehmann, was telling the Australia crowd to send Stuart Broad home crying," Bairstow wrote in his Telegraph column. "I'm sure it was not meant maliciously but for Australians then to say 'do not boo these guys' is interesting.
"It has to work both ways, it can't just all be one way. I'm not saying it is right or wrong. But to have the mentality 'we can do it to you, but you cannot do it to us' is a bit strange."