Dani -
So it's pretty likely that they first entered into a storm system, then they experienced all the problems.
Not sure there's enough information to conclude that.
We should therefore concentrate on arguing about why the crew should have entered a thunderstorm system.
The list of weather related aircraft accidents is way too long. There are still pilots who do not respect weather unfortunately. Guidlines are posted in all Flight Operations Manuals (or at least they should be !) on weather avoidance. When you are able to answer your question, "Why?", we will have made progress. Many pilots are "afraid" to carry extra fuel to avoid weather along their planned route because of fuel monitoring programs in place at some airlines. Others are 'management' pilots who think they're doing their company right by saving the fuel. Deviation fuel is cheap insurance.