Sorry for necromancing this, but I've been reading too much about Minoans to leave this alone.
The fact they didn't fortify cities is going to be a huge problem.
I think there's increasing evidence for Minoan fortifications. And in any case, their navy was probably a wall of its own.
Also, there's actually some plausible evidence the Minoan language may have been Indo-European after all. According to at least one guy who's reliable (not a fringe scientist) Linear A and B are 90% similar, phonetically speaking. That is, the sounds represented by the scripts are mostly the same with a 10% difference. So with the limited reading ability for Linear A, it provides enough evidence to assume it might be an Indo-European language, but of a different sort than Greek, rather it has more similarities with Sanskrit and Armenian. At least, this is the conclusion of
this site. It seems plausible enough, although I will admit I know little to nothing of linguistics, it seems quite believable and for the purposes of an AH thread it might be best to go with this.
However, one question I did have is how similar were Mycenaean and Minoan cultures? Would it be reasonable to assume they had similar forms of rulership to some degree? Because I've been able to find details on how Mycenaean society was organized according to Linear B tablets, but nothing on Minoan. All the wiki is telling me in regards to this is that when the Mycenaeans took Crete they adopted many forms of Minoan culture, maybe even the bureaucracy.
As to how they survive, maybe just handwave the Thera eruption away, assume their navy remains intact, allowing them to continue on their trading ways. Perhaps they might establish a thalassocracy like that of King Minos in the story of Theseus, if this wasn't already the reality. If they maintain amiable enough relations with the Mycenaeans perhaps the Dorian invasion is averted outright, although this will massively change what Greece is like. Would be interesting to theorize on the possibilities of a continued Mycenaean civilization ruling mainland Greece and a continued Minoan civilization ruling the Aegean.