However Whitmarsh told the official formula1.com website that the first choice had been to keep Perez and find Magnussen a place elsewhere on the grid where he could learn the ropes for a year or two.
"I hoped and tried to find him (Magnussen) a cockpit," he said ahead of the season-ending Brazilian Grand Prix. "I even did a deal and shook hands with a team principal up and down this paddock - an absolute deal - but he stepped back.
"Even after 25 years (in the sport) I find that difficult to deal with - I know I shouldn't, but I am still hopelessly naive. I still think that if you look somebody in the eye and shake hands then that's a done deal," added the Briton.
"When it turns out like in the Magnussen case, then I'm shocked - and I tell myself 'learn, don't be naive'."
Whitmarsh declined to name the principal, although he said he wanted to.
McLaren, who are fifth overall and enduring their worst season since 1980, were known to have been talking to rivals Force India, Lotus and tail-enders Marussia about taking on the Dane.
Whitmarsh said the end result was that McLaren decided the 23-year-old Perez would have to go, even though the Mexican had done a 'decent job' and deserved to stay in Formula One.
The team felt Magnussen, who had impressed in the simulator and testing as well as winning the Formula Renault 3.5 series title, was an extraordinary talent they simply could not overlook.
Whitmarsh said he had told Perez there was no threat to his job from drivers already in F1, such as Brazilian Felipe Massa or Germany's Nico Hulkenberg, but only from youngsters within the McLaren set-up.
"If Kevin didn't exist, probably Checo (Perez) would still be driving for McLaren next season," said Whitmarsh. "But Kevin exists.
"My first choice for Kevin was to put him in another team and do a year or two and then bring him back. That was my first choice - and if that was not possible apart from some very small teams, he joined us."
Whitmarsh said Formula One risked a "vacuum of young talents" if men such as Magnussen were not brought in, just as Lewis Hamilton was in 2007, because "the problem with the sport at the moment is that money is doing most of the talking with most of the teams".
Sauber, Force India, Lotus, Caterham and Marussia have all yet to confirm their 2014 lineups but the majority will require drivers to bring funding with them.
(Reporting by Alan Baldwin in London, editing by Clare Fallon)
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