Hamilton leaves the Woking-based team at the end of the season having spent 14 years with them since signing as a 13-year-old.
He will join Mercedes on a three-year deal, where he will replace Michael Schumacher, who yesterday announced he is to retire at the end of the season.
McLaren had been privately confident of retaining Hamilton's services, and the team have been left very disappointed by his decision to turn his back on them for a new challenge.
In McLaren's 46-year history as a constructor only one driver has ever left the team for another Formula One team, only to return later.
That man was four-time world champion Alain Prost. The Frenchman spent his rookie season with McLaren in 1980 but left for Renault, only to return in 1984 and go on to win three titles.
Hamilton had said earlier this week he would be prepared to drive for McLaren again one day and team principal Whitmarsh would not rule out the possibility of 2008 world champion Hamilton following in Prost's footsteps, although he acknowledges such a scenario is a long way off.
Speaking after watching Hamilton record the second-fastest time in practice for Sunday's Japanese Grand Prix, he said: "Yes, certainly, I think it is a possibility. But he is joining a strong team in Mercedes.
"I don't think he will be coming back any time soon, I am sure they have a good contract and they will want to work with him.
"I don't think Lewis' intention is to hop from team to team on an annual basis and I am sure that is not Ross (Brawn's) intention either, but never say never, as they say, and let's see what happens in the future.
"I think people want to talk about it a lot obviously and we are trying to focus on doing the job we are here to do.
"The relationship between the team and Lewis is a good one, it is a respectful relationship between McLaren and Mercedes as we are competing and we don't have a problem with anything that has happened with Lewis' decision or anything else.
"In the future - and I don't think it will be in the short term - who knows?"
Even though Hamilton is leaving for pastures new, he and McLaren still have title glory to strive for this season. The Briton lies 52 points adrift of championship leader Fernando Alonso with six races remaining, including this weekend's race at Suzuka.
Whitmarsh insists the team are fully focused on delivering Hamilton a second title before he departs, and does not fear the 27-year-old taking any technical secrets with him to Mercedes.
"I think Lewis has been part of the team for a long time. I think he knows the people and what we are trying to do but I don't think there's any great secret in that, so I don't think it's a concern," he said.
"I think if I was pursuing intellectual property from other teams, I'd probably be going for engineers not drivers.
"Lewis is respectful of the team and what it's doing, and I think he knows we're going to do everything we can in the remaining six races to try and win some championships and I think the best way to do that is to work together, be open and carry on as you ordinarily would."
Hamilton enjoyed a positive day at Suzuka, taking the runner-up spot in both sessions, but is concerned at the pace shown by the Red Bulls of Mark Webber and Sebastian Vettel, who were first and third during the afternoon running.
"It looks very close but I am feeling comfortable in the car," said Hamilton.
"The Red Bulls seem quite quick, I think I could have matched Mark's time, but if Vettel can do that time in qualifying it's going to be very close between them, and their long runs were very strong.
"But this is the best car I have had here for a few years."