For instance in the UK they're busy trying to crack down on "extremism". The Prime Minister has given a speech about extremism where he actually said words to the effect of "For too long we have been a passively tolerant society where if you follow the law, we leave you alone". GCHQ is absolutely being mandated to find extremists. It's merely the next chunk of the slippery slope that started the moment the law changed to try and fight terrorists.
Is it? My understanding is that NSA was founded for intelligence and counter-intelligence purposes. Cold war. SIGINT. And that is what it still does, although the capabilities of international terrorist/criminal organisations have become comparable to the capabilities of many nation states.
CIA is also an intelligence agency, but human intelligence (HUMINT), not signals intelligence. FBI, on the other hand, has a primary justification of fighting crime. DEA is quite similar but focuses on drug crime, and ATF on alcohol, tobacco and firearms. CSI conducts mass campaigns against people with some intelligence in all countries, with sub-offices in CSI (NY) and CSI (Miami).
(I'm not American, but have learned this much about the American three-letter things, mostly from popular fiction.)
But I've always understood a part of counter-intelligence is to counter the intelligence gathering of an adversary, or I suppose ally as well depending on circumstances. Which is what you are saying with your second point. Therefore, there is someone to catch doing it, just in a broad definition of the term.
So to argue that "it's all the same" really does a disservice to the analysis here. It's not. In the past, we had clear lines of civilization: pirates and others who operated without being part of a nation-state were executed on the spot. Now, however, we want to treat anybody we meet as being all the same. That's a nice sentiment, but it ends up classifying ISIL as some weird kind of criminal organization, and it is most certainly not that kind of thing at all.
Besides, one country's buccaneer is another country's privateer. I don't think those lines were as clear as you seem to think.
The Taliban was a sovereign state that, for a basket of reasons, actively supported terrorist attacks on the US. The invasion of Afghanistan was a war.
Al Qaeda is not a sovereign state; they're a criminal organization.
What makes it difficult to prosecute Al Qaeda using US criminal procedure is the fact that they're mostly non-citizens, mostly operating out of the US, mostly in countries that are not especially cooperative with the FBI.
In fact, I think my counterargument says that the "grave problem" is the opposite of the one you pose. It's not that prosecuting Al Qaeda criminally risks corrupting the criminal justice system. It's that prosecuting them as a sovereign who we're at war with has demonstrably corrupted the military.
The US constitution even has provisions for it: Congress can call forth the militia to suppress insurrection.
When I said all collection was not wrong I meant targeted collection, with a warrant and some oversight.
Anyone having access to a database containing the information for large proportions of the population is being handed more power than humans should have over each other, more than enough to blackmail a few key politicians and keep things looking rosy for themselves.
We must remember that as far as I can tell, governments have always wanted to collect whatever they could about anybody -- citizen or not. I do not agree with this, but the tendency is not limited to one government or another. What's new in the equation is the vast numbers of commercial applications/services that also want to track your every move online in order to keep you as a customer. It's this collection/retention of data that governments are now tapping into. If nobody had kept anything past 2 or 3 days, there wouldn't be much to mine.