He could also facing serious punishment if police charge him with causing actual bodily harm.
The video of Stokes' attack has resulted in many English cricket legends publicly criticising the star allrounder, however, a fresh report from Morgan turns the scandal on its head.
While the video footage appears to show Stokes attacking two men, Morgan claims sources have told him the cricketer was "defending two gay guys" who were being verbally "abused" by the two men he attacks in the video.
"I'm hearing that Ben Stokes intervened to help two gay guys who were being abused by yobs, one of whom was armed with a bottle" Morgan posted on Twitter.
"Stokes has told friends he was incensed by the homophobic taunts, then saw the bottle being raised and decided to defend himself.
"Stokes obviously regrets what happened, but apparently his view is: 'They started it, I finished it. I was protecting those guys'.
"Police are aware of Stokes' version of events and are now trying to find the two gay men to corroborate what he's said.
"Stokes has told friends: 'The guy had a bottle in his hand and was threatening us. Was I supposed to wait until he smashed it in my face?
"People can obviously make up their own minds about the Stokes video, but his defence certainly raises new questions."
The huge scandal has left England's Ashes hopes teetering.
The scene in Bristol prompted a regretful response from ex-Victorian cricketer Darren Berry, who was with former Australian Test player David Hookes when he died from a king hit in January 2004.
"Sadly just viewed the damning video footage of the Ben Stokes incident," Berry wrote on Twitter.
"It brought back horrific memories for me. Nothing good comes of this."
Stokes' place in the Ashes squad could be jeopardised by criminal proceedings, while England will be under pressure to hand down a lengthy suspension. The 26-year-old broke his hand in the stoush.
The star allrounder's absence would be a massive blow to England's chances given his Ashes credentials.
He hit a swashbuckling century during his debut Test series in Australia in 2013. He has taken 26 Ashes wickets at 33.07 with his medium-fast pace.
"The Ashes are looking like being Lost even before England arrive in Australia," former England captain Michael Vaughan tweeted.
"Cancel England's flights please!" ex-star England batsman Kevin Pietersen tweeted.
Stokes was arrested on suspicion of causing actual bodily harm and released without charge on Monday, but remains under investigation.
Coach Trevor Bayliss has described the circumstances which led to Stokes' arrest in Bristol early on Monday as "very unprofessional".
Stokes is allegedly seen to throw punches at two men in a video that was published on The Sun's website on Wednesday.
In the 61-second video clip, the man alleged to be Stokes is seen to hit out and grapple with another man on the ground before seeming to throw a punch and fall to the pavement himself.
As the altercation continues, the man reported by the newspaper to be Stokes then throws another punch in the middle of the street and the person struck falls to the ground.
The England and Wales Cricket Board said: "We have seen this footage for the first time tonight - when posted by The Sun.
"There is an ongoing Police investigation, which will look at all available evidence, and we do have to respect that process." Vaughan defended Stokes in two now-deleted tweets.
"Seen the video of (Stokes). It's not good. But I would like to know why the kid swings a bottle at the start!?" Vaughan said.
"The video is awful viewing. (Stokes) shouldn't be in that position. But was he reacting & protecting 2 people from a random attack!" Stokes was included in England's 16-man squad for the five-Test series against Australia that starts in Brisbane on November 23.
- with AAP
