What now for British journalism? Once again its working practices are stained in the eyes of those who consume it, and once more it will face a humiliating and public examination of how it goes about its business. It will undertake that process shorn of one of its most famous names, the News of the World (NOTW), which has breathed its last and joined Today, the Daily Sketch and countless other national titles which exist now only in the archive of the British Library.

The NOTW is set to be replaced by a Sun on Sunday. It could even see its own 168-year-old masthead re-emerge Phoenix-like from the ashes of the hacking scandal, as there is interest outside News Corp in resurrecting the brand. But despite this, it is clear that journalism has been indelibly tainted by this shameful affair.

When "Her Majesty's Press" is next required to seek the assistance of citizens in compiling dispatches from the scene of a tragedy, it may find it harder than before to secure co-operation and make the case that it is performing a quasi-public service.

Crime reporters who are required to find the inside track on a police investigation are likely to discover that officers, wary of the uproar over News International's alleged payment of more than £100,000 to Scotland Yard officials, will decline even the most innocent of encounters.

And MPs, perhaps even local councillors, will fear getting too close to the media. Already wary after being stung by journalists over their expenses claims, elected officials can see that cosy relationships with the press can be just as damaging.

Bob Satchwell, the executive director of the Society of Editors, asks the public to recognise that there are 20 national newspapers and 1,300 regional ones in Britain, and not judge all reporters by the standards of a few. He also says people in positions of authority should not be afraid to maintain relationships with journalists. "There's nothing wrong with the odd cup of tea or pint of beer or being invited to lunch," he says.

There must be a real risk that British journalism finds itself weakened and marginalised by the backlash, leaving it closer to the poodle of a French press that consistently fails to hold those in power to account. "The fallout from the phone-hacking affair will be felt by journalists well beyond Wapping," says Ian Reeves, a lecturer at the Centre for Journalism at the University of Kent. "The danger is that the public's justifiable anger over the hacking of Milly Dowler's phone ends up blinding them to the importance of a free and robust press."

Reeves also fears the damage inflicted on the entire news media by the hacking scandal will "strengthen further the invidious influence of the world of PR".

Publicists and communications specialists have already seen their status, relative to journalists, increased by the difficult commercial conditions under which most media companies operate. The muscle of the PR business in restricting press access may already have been a factor in the behaviour of those desperate NOTW workers who were prepared to break the law for a scoop.

Mark Borkowski, a prominent PR professional, says: "It's quite hysterical that a publicist or PR man can now say that journalists' reputation is worse than theirs. It's going to give grubby PR companies – those laundering reputations – more power."

Equally damaging is the potential effect that this scandal will have on younger generations. With many teenagers disengaged from the traditional news media, few will see any reason to become the readers of the future in the light of such scandalous behaviour by its professional proponents.

Bright graduates are hardly likely to be attracted to a trade that is already struggling to offer the financial rewards of traditionally comparable sectors.

Yet, despite all this, George Brock, a professor in journalism at City University, London and a former senior executive on The Times, believes that good can come out of the episode. It was, he points out, other journalists who brought the scandal to light.

"I don't think all of journalism is in crisis," he says. "What we've reached is the end of the road for anything-goes, dog-eat-dog journalism practised in some – note, some, and not all – daily newspapers.

"Either those bad practices are going to die out because of exposure or they're going to be reined in by enhanced regulation," he adds.