Yes, it is a sign that the Dead Men are going to help, although it's not clear at the time it happens.
The avalanche is a sign that the Dead Men of Dunharrow are choosing to fulfill their oath to the King of Gondor (Aragorn), which will free them from their curse.
Why destroy their city in the Dwimorberg, along with the ossuary where their remains were kept? First of all, they won't be returning there. Secondly, they would not be sentimental about it, since it was a sort of prison for them.
Their skulls being released from the ossuary foreshadows the oathbreakers being released from the curse after they help Aragorn. It can be seen as the beginning of the work that's completed when Aragorn finally releases them from their oath, and their spirits fade away.
The skulls do belong to the Dead Men.
Isildur's curse did not extend the lifespans of the Dead Men -- it only prevented their spirits from leaving Middle Earth. So their physical bodies would have died about 3000 years prior to the events of LOTR. The oathbreakers were not completely uncivilized, so we can assume that placing the remains of their dead in the large ossuary wall was part of their burial practices.
When we see the skull avalanche in the movie, we don't know if the Dead Men are trying to kill Aragorn & co., or if something else is going on. It's presented ambiguously on purpose, to create tension, similar to the laugh of the King of the Dead.
After we learn that the oathbreakers did decide to help Aragorn, we can look back at the event with a greater understanding.
I do agree that the scene is confusing and should have been left out. As most people here know, it was not included in the theatrical release.