Honda and Casey Stoner discussed the two-time MotoGP champion replacing the injured Dani Pedrosa, but the downside of a short-term comeback outweighed the positives.
Stoner won titles in 2007 with Ducati and 2011 with Honda before retiring from MotoGP at the end of 2012, aged 27.
While he has not raced on two-wheels since, the Australian has remained one of the Japanese manufacturer's test riders and will contest July's Suzuka 8 Hours.
Pedrosa is set to miss at least the next two races after undergoing arm surgery in Madrid on Friday, with HRC tester and 2009 250cc champion Hiroshi Aoyama to stand in.
Stoner tweeted on Friday that "it would have been an honour" to replace Pedrosa, but team manager Livio Suppo told Italian newspaper Gazzetta dello Sport it was never a realistic proposition.
"Yes, we have talked about it," he said of potentially using Stoner.
"There were some pros, but more cons, so we decided it would be better to leave it.
"People don't realise how high is the level [of competition]. Having won a lot doesn't mean one is immediately quick on his return.
"Casey doesn't know the upcoming two tracks, and in the last two years he has only run for four days with this bike.
"I understand a return may spark people's imagination, everyone would have liked it, but what if he wasn't quick? What would people have said and written then?"
Suppo highlighted the tough comebacks endured by Michael Schumacher in Formula 1, and more recently Stoner's countryman, Troy Bayliss in World Superbikes.
A three-time WSBK champion, Bayliss recorded a best result of ninth last month in a two-event cameo, after six seasons away.
"Casey is Casey, but do we really think he may trouble Marc [Marquez] these days?" he said.
"Troy, too, was convinced he was going to [the WSBK round in] Thailand to win. When I heard he was returning I sent him a text message and he replied 'Death before dishonour'.
"Riders are a bit crazy sometimes, but in the end I think the one who was left more disappointed was himself.
"Another example is Schumacher: he finished his career at Ferrari with a spectacular recovery in Brazil, while on his return with Mercedes he struggled to get one podium.
"At this time it's better to stay out of trouble for no reason."
Suppo did, though, leave the door ajar for Stoner to appear in MotoGP this season, if he is sufficiently motivated and prepared.
"If he seriously wants to return, he must prepare," he said.
"Entering a one-off race would be more of a disadvantage, for us and for him, with the added risk of getting hurt. And anyway, I keep on believing that he doesn't want to race full time.
"A wildcard entry at the end of the season? He can ask us and we'll think about it."
Translation by Michele Lostia