I'm not really sure the comma adds anything.
I see that I overlooked some of your questions in my previous reply. I think that (1) is correct as it is, if we accept that "to freak one out" is proper English. (I say it, so it must be!) Structurally, it is similar to:
3: It's frustrating having to answer these same questions yet again.
And yes, the first "it" is a dummy "it". (2') is a proper paraphrase of (1), and is definitely grammatical.
1, second version) It's freaking me out, just thinking about it.
Anyway, what kind of horrible world would this be if someone who was already so distressed had to worry about proper comma placement on top of everything else? It's freaking me out just thinking about it!