Four PSNI officers were injured after they came under attack with heavy masonry, bricks, bottles and fireworks during trouble which flared overnight in Carrickfergus.
It followed a largely peaceful protest over Belfast City Council's decision to only fly the Union flag on designated days.
The constituency office of Alliance MLA Stewart Dickson was ransacked and destroyed by fire.
Three arrests were made, including a 20-year-old woman who appeared in court on Thursday charged with riotous behaviour, assault on police and resisting arrest.
Two teenagers - a 17-year-old girl and a 15-year-old boy - have since been charged with affray and unlawful assembly, also in connection with the disturbances in Carrickfergus.
They are both due to appear before Belfast Youth Court on Friday morning.
Commenting on the trouble, Superintendent Philip Knox said: "Officers who had come out to do a day's work, protecting the community, found themselves under sustained attack from masked thugs. This is completely unacceptable.
"We are in no doubt that there was a degree of orchestration to the disorder. People came armed with fireworks, they had balaclavas and masks in their possession. Those intent on peaceful protest have no need for such items."
What we have seen in the past few days is not acceptable. It is an outrage to have democratic parties intimidated and burned out simply because they took a democratic decision. It is wrong.
Chief Constable Matt Baggott
Meanwhile in Bangor, councillors Michael and Christine Bower had the front window of their home broken by a paint bomb.
They said it was lucky their 17-month-old daughter was not playing underneath.
"An attack like this on the home, just above where my daughter could have easily been playing, where her toys were gathered in the room, makes this all the more disturbing," Mr Bower told UTV.
"It doesn't bear thinking about the consequences had she been there."
North Down MLA Stephen Farry said there was also an attempted arson attack on his constituency office in Bangor.
"Petrol or some other accelerant was poured over my shutters by a number of people," he said.
"Fortunately, they were interrupted by a passing police patrol and fled the scene. I am grateful to both the police and the fire and rescue service for their assistance."
A flag protest also took place in Lurgan.
Police said a "mob" of around 100 people descended on Carrickfergus town centre in the wake of a peaceful protest involving up to 1,500 at Irish Gate Roundabout.
Missiles were thrown at officers and buildings and an Alliance property was burnt out.
Riot police fired a number of baton rounds as they dealt with the disorder, which started after 7.30pm. Two men and two women have been arrested.
"This was an extremely reckless act and put the lives of the residents living in the vicinity in very real danger," Superintendant Knox continued.
"It is only through the swift actions of police and Fire Service that the fire was contained and extinguished and a tragedy was averted.
"We will be focusing on identifying those involved in the violence as well as those who may be responsible for organising it and bringing them to justice."
Loyalist protests have also taken place at Alliance offices in Belfast this week.
It comes after the City Council passed a proposal to restrict the flying of the Union flag at City Hall, which the party put forward.
Alliance has requested that the Assembly be recalled in light of the violence.
Mr Farry continued: "An orchestrated campaign of intimidation against Alliance elected representatives has unsurprisingly turned violent. We in Alliance will remain resolute in standing up for values of a shared future, democracy and the rule of law."
Political parties have condemned the trouble.
DUP East Antrim MP Sammy Wilson said: "People are entitled to peacefully protest but there is absolutely no justification for the carnage which has been caused in Carrickfergus this evening. Those involved do a disservice to the flag they claim to defend."
Sinn Féin Deputy First Minister Martin McGuinness said: "The attacks overnight are wrong and need to be condemned outright. There is no justification whatsoever for these type of actions."
UUP leader Mike Nesbitt said: "What unionism needs today is brains, not brawn. We need an analysis, a strategy and an agreed outcome."
TUV leader Jim Allister said: "The great political and constitutional wrong done to the Unionist majority in Northern Ireland by the Alliance Party delivering the Sinn Féin agenda of denuding the capital city of its daily expression of its Britishness does not warrant or justify violence, rather it calls for a sustained political response."
SDLP leader Alasdair McDonnell said: "Stewart Dickson is doing his best for the people of East Antrim and an attack on him is an attack on everybody in East Antrim."
On Monday night 18 people were hurt when violence flared in Belfast following the passing of the Alliance motion. First Minister Peter Robinson described the scenes as "totally unacceptable".
Police in Carrickfergus liased with local community representatives in their effort to restore calm.