Presentation thesis help?

I would not use the word "cult" so many times in the first three sentences. Also, you don't really have a thesis sentence- you never explicitly state a view. The last sentence in the paragraph doesn't make grammatical sense. I would be a lot more interesting is you opened up with a very brief story about a cult that ends badly to illustrate your point. I think that the third sentence is an over statement and should be made less harsh.

I would write it more like this: (I'm not sure if the KKK may be considered a cult, it's just an example paragraph) In the post-civil war south, the Ku Klux Klan (cult) terrorized society through executions and other acts of terrorism. Although not all are violent, cults have committed some of histories most shocking crimes. Often, once these crimes are committed, it is too late for law enforcement to aid (you may want to mention the case of the man who poisoned his several-hundred person cult). The difficulty is the fine line between preventing these tragic crimes, and preserving freedom of religion. The present essay analyzes cases of cults resulting in tragedy and considers if Freedom of Religion has been taken too far.

Cults have been around for as long as history recalls.

Oh really. You should add "since the dawn of time," while you're at it.

Some of history's most shocking crimes have come from cults.

Vague, unsubstantiated.

Cults and cult practices have never failed to challenge the justice system.

You shouldn't speak in absolutes. And what does "challenge" the justice system really mean?

Law enforcement can only step in after the law has been broken and in the world of the cult, this is often too late.

Too late for what? Do you mean the law can only step in after someone is dead or hurt? The law can charge for conspiracy, you know. They could have charged the guy for even preparing to start making the kool aid. It doesn't sound like you understand the law and the options law enforcement has too well. There are prophylactic laws, too, that prevent certain things cults do that have not been held as protected by freedom of religion. If you do understand that, what are you saying is too late, then? Are you saying you should be able to stop somebody from thinking about something? Stop them from associating with certain people? Put them in jail because they have certain beliefs? Who is going to judge what "beliefs" are acceptable?

While most of the cults end up in a disaster,

Really? What is a disaster? Do most cults really end up in one of these so-called disasters?I haven't seen any cults having a disaster in the headlines recently, yet apparently cults exist. Is it a disaster if members of a cult go out into the woods, stand naked, and sing the song from Barney? What if they chant mumbo jumbo and kiss crystals in the privacy of their home?

it poses the question, 'Has freedom of religion gone too far?

Too far? Too far into what precisely? What is happening lately that is "too far?"

A sound thesis you're on a good track. First let me say it was choppy, the sentences could flow a little better. Second, give a few vague examples of the types of cults you're talking about, then in the body paragraphs go into more detail. This will help because your readers get a vague idea right away where you're going with your paper. Also you might want to give a quick definition of cult since others have their own interpretations of what cults are. Best make your meaning crystal clear. Good job so far

You're kinda just repeating the obvious, get more specific.