Pietersen hinted that the current series against South Africa could be his last in international cricket, despite showcasing his good form with a century in England's first innings of the second Test at Headingley.
However, former captain Stewart believes that the batsman could be replaced if he decides to finish his career in an England shirt.
Stewart told BBC Sport: "I don't see it as a huge issue for captain Andrew Strauss. This is a problem above his head, for the likes of ECB chairman Giles Clarke, chief executive David Collier, managing director of England cricket Hugh Morris and team director Andy Flower to resolve.
"It's important to stress that no player, however good, is bigger than the team, and no one is irreplaceable. Granted, it may take longer to fill the boots of some more than others, but there will always, eventually, be someone to step in."
Pietersen retired from limited-overs cricket with England earlier this summer.