The Ongoing Struggle With Civil Liberties

Recently while reading over a few posts in the editorial section of the online Chicago Tribune, I came across an article on the new legislation passed regarding how to handle terror suspects. Having the perilous times unit still fresh in my mind, I finished reading the article and realized how much of a problem the restrictions on civil liberties actually are. The article stated that the Republicans in Congress wanted to, "decree that anyone connected to al-Qaida could be held only in military custody, not tried in civilian courts — even if the detainees were U.S. citizens captured on American soil".
Now at first when I read this I believed that the Republicans were crazy, and how could you step on the Constitution by even thinking this? However, after thought on the debates within class during the presentations, especially the war on terror, I realized that the problem isn't as clear cut as it should be and views like this aren't as radical as they seem. My gut instinct is to protect the Constitution at all costs, but when American lives are being lost at the hands of terrorists I also believe everything needs to be done to stop those doing it. An ongoing struggle in my mind in what's right and wrong, and one in Congress also, the restrictions on civil liberties are a hard choice to make and at this point it looks like it will be a while before they are resolved. Civil liberties are a touchy subject because no President wants to leave a bad mark on history taking away the rights of Americans. The legislation that was just passed didn't change much, it just solidified the abilities of the government that were already in place, including the right to take a citizen of the street and detain him for the rest of his life with no chance of appeal. 
What is too far? Is there anyway to solve this problem or will it always be an American issue?