Well, that's similar to what I have been thinking before.
Of course it is.
About the first comparision: An organisation - if there is evidence that it is evil - has to be destroyed, of course, but killing its members should be avoided, and they should be imprisoned instead. Since the Makuta obviously can leave their armor at any time and possess a new body, it might make sense to seal them in Protodermis, like Teridax 1000 years ago in "our" universe. If there's no other choice, that's a different thing of course, but it doesn't look that way...
About the second comparision: I wouldn't like our state to observe me and all the other people, just because there might be one or two potential terrorist somewhere in their country... That's nonsense. A few weeks ago, there was a scandal in Germany, when some people found out that Lidl, a chain of stores, hired detectives and installed cameras to observe their cashiers and all the other people who worked for them (and customers, of course)...
About the third comparision: I can't really say anything against or in favor of this, since an important information is missing: Will the Dark Hunters simply be unable to do anything bad anymore after that (in prison, for example)? Or will they themselves will be smashed, just like their operations? ;P
I think that both things you suggest are correct. In my opinion, Tuyet - and all politicians who would act the same way in the first two cases - indeed trys to keep peace... in an evil and corrupt way. Other people might think different, of course...