Northern Ireland's Deputy First Minister also suggested his party could withdraw its support for policing in Northern Ireland if Mr Adams is charged.
Such a move would be a massive blow to the peace process.
Mr McGuinness also said he expected police to ask for Mr Adams to be held for a third successive night of questioning about one of the most notorious cases of The Troubles.
The 65-year-old vehemently denies allegations by former republican colleagues that he ordered the murder and secret burial of the mother-of-10 in 1972.
Mr McGuinness accused Northern Ireland police of arresting Mr Adams in a bid to hurt Sinn Fein.
Asked if his party would withdraw support for policing if Mr Adams was charged, Mr McGuinness said: "We are very thoughtful and we are very reflective but I think if such a scenario does develop then we will sit down and we will reflect on what will be an even more serious situation than the one we face today."
Sinn Fein's decision to sign up to support the police in 2007 was viewed as a milestone in Northern Ireland's recent history, prompting the return to devolved rule and the party entering power-sharing government with the Democratic Unionists.
Republicans have hit out at Mr Adams's detention three weeks before European elections but Downing Street has denied the arrest was politically motivated.
In addition, Northern Ireland's justice minister said yesterday he could see no sign of dark forces operating within the police force.
Alliance Party MLA David Ford said: "If there are dark forces within policing, I can see no sign. I see a police force with very high levels of confidence, higher than the Garda Siochana [Irish police] or many forces in Great Britain, and I see a police force carrying out its duties properly and appropriately."
Ireland's deputy prime minister Eamon Gilmore also said that politicians should not receive special treatment when it comes to police investigations.
Meanwhile, Tory-LibDem ministers have admitted they do not know how many royal pardons have been granted to IRA terrorists because 10 years of records are missing.
The admission came as they revealed more than 350 amnesties had been issued in Northern Ireland over the last 35 years. The total could be much higher, however, as data for the decade between 1987 and 1997 cannot be found.
Labour MP Kate Hoey accused ministers of a "cover-up" and said that she had been "shocked" at the disclosures.
"I find it unbelievable that so many people in such a short space of time were given pardons," she said. "I want to know who all these people are. I think that the public will want to know who these people are."
Miss Hoey, who said she would be pursuing the issue in the Commons, questioned why the pardons had not been listed in official published documents at the time, as would normally be the case.
She also called on the Northern Ireland Secretary Theresa Villiers to explain how such important records could have been lost.
"There was clearly a cover-up," she said. "How can records not be found on something that the Queen has to sign off?"
The Northern Ireland Office said the issue related to former governments, and no pardons had been granted since the Coalition came to power in May 2010.