The South Africa-born Pietersen quit one-day duty for his adopted country this month when he was told by the England and Wales Cricket Board (ECB) the terms of his central contract would not allow him his wish of abandoning 50-over one-day matches while still playing Twenty20 internationals.
Pietersen had been settling well into the role of opener and ended his ODI career with back-to-back hundreds against Pakistan.
But England will begin one-day life without him in a three-match series against the West Indies starting at Southampton on Saturday, with Ian Bell set to take Pietersen's place at the top of the order.
Pietersen's exit comes as West Indies welcome back a star opener of their own in Chris Gayle, following the former captain's 15-month exile from international cricket due to a dispute with Caribbean cricket officials.
"If you look at when Gayle has been away, we missed our best player," Gibson said Thursday.
"It's a big thing to lose your best player. KP has been good in the last two one-day series and they were trialling him at the top of the order.
"It seemed it was going to work but now they have to put someone else in that spot and hope that person has the form KP had.
"Bell is very different and he is also a very capable replacement. We know we still have to work to get him out."
Former England bowling coach Gibson added: "Nothing KP does takes me by surprise. He is his own man and does what he wants to do whenever he wants to do it. That is his character.
"I am sort of surprised he is in such good form and chose to walk away from a format he likes...When he is sitting at home watching on TV he might miss it."
Pietersen, 32 later this month, explained his decision to quit white ball internationals and now play just Tests for England by saying: "I can't play at my peak -- I can't keep on playing every single game and enjoying every single game -- when I have to play every single form of cricket, or when I have to train every single day.
"You fall out of love with it," added Pietersen, the married father of a young son. "And I want to play cricket until I'm 35."
Pietersen's move was defended by England off-spinner Graeme Swann.
"There comes at a time when you get towards the end of your career, into your thirties, when something's got to give," Swann told the Cricket Paper.
"You can flog yourself to death and fall to pieces or you can start to be quite wise and make a pragmatic decision.
"Whatever Kevin's made his decision for, whether it be financial matters or the family or whatever, I can understand where he's coming from because there's certainly times I look at a schedule and just think: 'How can I do this? My body's killing me. I haven't seen my kids, my wife is ready to get up and walk out because I'm never here.' We're human beings at the end of the day."
The 33-year-old Swann added: "I can understand where Kev's coming from and I can understand where the ECB are coming from at the same time: 'We pay you well, we expect you play, it is a short career.'
"But people have to face facts that you are in control of your own destiny, so you decide: 'I've had enough, I'm going to retire from whatever form of the game,' then that's it." AGENCIES
