News of the move, which is set to be confirmed today, has surprised many observers who question why the longest serving coach in the Pro12, who has steered Glasgow into play-off contention, is effectively being sacked.
It's understood Sean was offered a role as head of acquisition for Scottish Rugby, as well as working with the national U20 squad.
Glasgow’s defence coach, Gary Mercer, is also to be replaced, by Queensland Reds assistant, and former Scotland ‘A’ flanker, Matt Taylor, who will have a shared role with Glasgow and Scotland.
Sean told the Herald: "I was brought in and told this change was going to be made, and here's another opportunity to stay in Scottish rugby.
"I was given a great opportunity nine years ago when I joined Glasgow as backs coach and I've had a great nine years here. Gregor's getting that opportunity now."
With the Warriors in contention for the RaboDirect Pro12 play-offs for the second time in three years the there's a danger the news could demoralise Glasgow players, management and supporters, but Sean says he's determined to prevent that from happening.
"The timing's a bit awkward but we've just got to deal with that," he said.
"It was a relief to get the chance to discuss this with everyone in our set-up, many of whom I've worked with for a number of years, before they found out from elsewhere, because none of them had read the paper it appeared in before I spoke to them this morning.
"They're all pretty shocked, but I said to them that this is professional sport and it's always going to happen sometime. It might have happened last season when, although there were reasons for it, we struggled, so I'm glad that we've been given this chance to show what we could do with a stronger squad.
"I'm leaving Glasgow but I'll be giving it everything to make sure we get into the play-offs. I hope everyone who cares for the club will do the same because this is a time when we need to support the players.
"Coaches come and go. Everyone moves on at some stage and I'm the longest-serving coach in the Pro12 so I was next.
"I'm proud of the players we've brought through at Glasgow, the likes of the Lamont brothers, the Evans boys and Richie Gray, and the role I'm going to be given is to identify talent throughout the world.
"We will now be doing that professionally in the marketplace, selling Scotland to the wider world. That is something that I can really look forward to doing because I believe I can do it well."