I've just got back from Crete. Had every intention of running 3-4 times in the week I was there but actually only managed one run. It's as safe as running anywhere else. I ran down by the harbour in Agios Nickolaos and it was stunnning compared to my usual runs in Lancashire.
I was out at 8.00am and even thought it was quite cool for May and especially cool compared to the summer months, I was sweating like a loon by the end. If you go, i'd go early.