While 全然 is often used in positive sentences these days, this adverb is still basically a negative polarity item, and it has a strong affinity for a following negative expression within the sentence. This means, in this case, 全然 modifies 思わない, "I don't think at all (that ...)" regardless of the space or comma after it. This is also true in conversations where you cannot use commas. The sentence has the same meaning as 綺麗だとは全然思わないよ. (Of course commas can disambiguate things in some cases, though)
To say Sentence 1, you need to choose another adverb and say, for example, "すごい綺麗だとは思わないよ" or "100%綺麗だとは思わないよ". Actually these are still ambiguous, but at least these tend to mean 1 simply because most (non-NPI) adverbs modify something right after it.
EDIT: As l'électeur pointed out, 全然 can modify 綺麗 in a rare context where someone has just used 全然 clearly in a positive sentence. In such a case, 全然綺麗と is a direct quote and the sentence would mean something like "全然綺麗 is an overstatement". But it's still much better to disambiguate using brackets in writing, like:
EDIT: Please also recheck the usage of 全然 in positive sentences. Read Boaz Yaniv's answer in your link. 全然 in a positive sentence is used to negate someone's prior expectation, and it rarely translates to "completely".