Civic groups critical of Samsung complained that independent counsel Cho Joon-woong failed to indict Lee for the alleged bribery and levied the other charges without arresting him.
Cho told reporters in releasing the probe's findings that taking Lee into custody was too big a risk for South Korea, citing "the extremely competitive global economic situation."
Founded 70 years ago by Lee's father, Samsung Group has interests in shipbuilding, insurance, leisure, apparel and dozens of other businesses.
Samsung Electronics, its flagship, is a world leader in computer chips, flat-screen TVs and mobile phones. The conglomerate's construction arm is erecting in Dubai what it touts as the world's tallest skyscraper.
Cho's sentiments were echoed by ordinary citizens in South Korea, where Samsung companies account for up to 20 percent of the country's exports, by some estimates.
"Of course proper legal process should be followed, but I do not want the foundation of Samsung to be shaken," said Min Tae-sik, a 57-year-old engineer. "I am a little bit nervous, actually."
Lee, widely seen as the driving force behind the rise of Samsung Electronics into a global force, hinted last week that he might resign over the scandal.
Kim, the Yonsei professor, said such a move was unlikely to occur anytime soon, even with the indictments.
"Unless he's sentenced in court, I don't think that's going to happen," said Kim, who estimated it could take up to two years for a verdict.
Still, some said the charges that were filed -- which potentially carry prison terms -- sent a strong signal to Samsung and the rest of the country's business elite.
"This will have an effect," said Michael Breen, longtime British resident of Seoul and author of a book on South Korea. "I think anything of this scale that happens with Samsung becomes a lesson for everyone else."
Investors, have generally taken a low-key approach to the scandal, pushing up shares in Samsung Electronics, for example, by some 25 percent since it broke in early November.
"I think they expect things will be handled much better in the future," said Lee Jae-hyok, a technology industry analyst at Daiwa Securities SMBC in Seoul.