Yeah myself and a friend are just doing a long weekend Friday-Monday (it's replacing a cheap Gran Canaria trip posted further back). I don't think you can book these bargain hotels as part of any packages, so it looks to be a flight + hotel separate booking if you were to go for it.
It goes without saying that it's a risk at the moment when it's not ATOL (package) protected.
If Greece goes onto the quarantine list, then I'd hope TUI would refund the hotel.
Our flights are with Jet2, and they are cancelling flights to countries whereby there are restrictions in place, so again I'd hope the flights would be refunded without too much hassle.
Ultimately for 3 nights all inclusive with perfect weekend flight times, it's only costing us £140pp, so worst case scenario is we would lose that which is a relatively small gamble financially.
If you're looking to go for longer, and ultimately have a larger financial gamble, then I'd say book your flights with Jet2 where possible (as Ryanair/Easyjet/Wizz are all still flying to countries against FCO advice so you'd be on the hook for the flights), avoid mixing airlines (out Jet2, back Ryanair for example) and pay by credit card for the hotel and flights for that extra protection, but obviously be prepared for things to fall apart at any moment!
FWIW I think/hope Greece will be ok now. Their cases are dropping and less people are travelling now it's coming out of peak season. Please don't quote me on that though ;)