I have been away for a while and have missed this whole Islanders-vs-Pirates thing. Does anyone know if I'll be able to join a side before this plot is ending? Cause I really want that trophy (AND access to the Omen isles)

The RS war has ended so I don't think you can join a side :(

Nope, you can't join a side now. Sorry. :( You'll have to wait now until the plot is over to get access to the Omen Islands.