For nearly four years, a key alliance has driven the ambitious expansion and revamp of the Guardian – the close tie between editor Alan Rusbridger and chief executive of the parent group Carolyn McCall.

Now, as costs of that expansion come under increasing scrutiny, that alliance has been broken with this week’s news of the sudden departure of Ms McCall to head low-cost airline EasyJet.

Her departure was described by one fellow executive as “something we thought would happen, but hoped wouldn’t”. Most had expected her to stay on to make important decisions, such as the timing of the sale of its 50.1 per cent stake in the online car sales business Trader Media Group, which could come next year.

Guardian Media Group, supervised by the charitable Scott Trust, was established to run the newspaper business and other divisions, such as radio, local papers and a portfolio of broader media investments to ensure the “survival of Guardian journalism in perpetuity”.

It is a mission statement that led the group to team up with Apax, the private equity firm, which is a partner in Trader and the business-to-business company Emap, while the core newspapers lose money.

In common with most competitors, they have struggled to find ways of compensating for the advertising downturn and the decline in circulation revenues.

Criticism of Ms McCall’s time in charge of GMG has fallen into three main categories. The first is that capital expenditure such as spending £80m or more on Berliner presses – a half-way house between tabloid and broadsheet format – was wasteful at a time of decline in the industry.

The second is that she has allowed Mr Rusbridger, also editor-in-chief of The Guardian’s Sunday sister paper The Observer and the internet edition, to adopt a policy of free content online when others are exploring paywall options.

The third is that building up a portfolio of investments such as Emap and Trader to provide medium-term capital returns, but no cash at a time when the newspapers were losing money, put the whole group at risk.

“The Berliner press move was a spectacular error,” said Tim Luckhurst, journalism professor at the University of Kent.

“I don’t think they sell a single copy more now because they are that size. It was £80m down the Swannee. Not a great business decision.”

The change to Berliner format in September 2005 was initially a huge success, boosting circulation to 370,000, up 8 per cent on a year-on-year basis, in its first six months at a time when its formerly broadsheet rivals were all losing sales.

The effect was not permanent, however, and now the Guardian has fallen back to 284,000.

One of Ms McCall’s senior colleagues countered that the Berliner move accelerated the need to buy new presses by only two years and that neither The Independent or The Times, as tabloids, nor The Daily Telegraph, which remained broadsheet, have fared any better on circulation. The Guardian enjoyed a two-year advertising benefit as the only paper printed in full colour.

The online strategy remains controversial. Mr Rusbridger says that all their research has suggested that they could not put their general news behind a paywall, as Rupert Murdoch’s Times announced on Friday, without smothering its journalism.

Douglas McCabe, analyst at Enders, said. “There is certainly an ambiguity between a strategy that is very focused on an online future and simultaneously on a very expensive print future. It is betting big on both worlds simultaneously.”

Overall, though, Enders believes that Ms McCall, 48, who was involved at all stages in the portfolio decisions, has struck the right balance.

Although the newspapers lost £37m in 2008-09 and will perform about the same in 2009-10, action to reduce costs will begin to show through next year and, if advertising rebounds, the analysts say the investment portfolio should be easily big enough to cover future losses unless there is a double-dip recession.

GMG has £260m in liquid assets and its 50.1 per cent in Trader could raise a further £500m to £600m. The exit from Emap, where revenues have fallen 15 per cent since their peak in 2008 and earnings about 7.5 per cent, is further off, perhaps mid-decade.

Mr Rusbridger, according to a person close to him, understands that he has a responsibility to control editorial costs so that the £260m is not used up. In that event, the sale of the Trader stake would become a matter of necessity rather than choice.

An external replacement of Ms McCall might disagree with his central tenet of free online content. “But that assumes that the board would appoint someone who doesn’t sign up for Alan’s beliefs, which seems unlikely to me,” said a person who has attended GMG board meetings. “If his and Carolyn’s bet is wrong, he and the Scott Trust will have to all go down together.”

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