no offense but this post is born out of ignorance.
What you're saying would be akin to the United States IGNORING several of it's Generals, Colonels, and varying "grunts" all leaving the US Armed Forces and joining a group like Al Quada (sp) (imagine if Al'Quada didn't attack the US..but still did EVERYTHING ELSE they do) and saying that the US should just let them go and have no kind of ties or obligation to stop them.
It's "cool" to root for the bad guys now-a-days isn't it?
No if this happened the US WOULD be obigated to stop those men that THEY TRAINED from doing harm to others...it's NO DIFFERENT.
Is the Federation perfect? no. But your reasoning and examples make no sense and, no offense, are not well-thought out at all.
The Maquis may not attack the Federation, but they are FILLED with ex-Fed OFFICERS that were TRAINED by Starfleet. So YES, the federation DOES have reason and an obligation to stop them. Afterall the federation are the ones that TRAINED those men to DO WHAT THEY ARE DOING.