First, as someone else pointed out, ISIS & AL Qaeda are declared terrorist organisations in many countries, not just the USA, so members of those organisations can and would be arrested and detained. I can't really express an informed opinion about how protests are "managed" in the USA. In Australia, in most jurisdictions, a permit from the relevant local Council is required to have any form of rally, so if you want a hypothetical, then the "Friends of ISIS & AL Qaeda" ( because those organisations, ISIS & AL Qaeda are declared terrorist organisations so they will never get a permit to do anything, except go straight to jail ).. The "front" group would have to get a Council permit to hold their rally/protest, to get the permit they'll need "public liability insurance".. and that will be extremely difficult to get. Then the local Council can probably refuse the permit on the grounds of risk to public safety. So assuming as a hypothetical question that a " front" group managed to get a permit to hold a political rally/protest, and it's so unlikely as to be a "never going to happen", and more than three people and a three legged dog turned up to support the political rally/protest then if outraged members of the public tried to prevent the rally/protest going ahead, and attempted to do so with violence, then those outraged members of the public are not evil, just stupid for allowing passion to overrule common sense, and I suspect that most Police would act to deter and prevent them from committing any act of violence, and if the omotps ( outraged members of the public, plural) complied with the Police directives I think most Australian Police would " let them go with a caution"...it's only when an omotp actually assaulted a Police officer that an arrest is likely. Or if an omotp actually assaulted another person, and the assault was witnessed by a Police officer, then the Police have no choice, they have to take action.
There has to be rule of law. In Australia it's an offence to encourage violence or racial discrimination.. I'm a bit vague on the specifics, but if a "front" group was having this hypothetical rally, then any offending signage constitutes an offence, so that gets confiscated and an infringement notice with fine is issued, any speaker who "says the wrong thing" gets shut down and reported, charged and prosecuted, if they keep making offending remarks they get arrested.. By violating the conditions of their permit to hold a rally, they "void their permit" and get shut down immediately.
So, quite frankly, your abstract hypothetical is in all practical terms, in Australia, just never going to happen in real life. And rightly thus.