Air Malta has one base in Malta and one in the UK as far as I know. apart from the problems being posed by a bunch of pilots leaving for the likes of Emirates and Qatar, there is also the looming problem of low-cost operators soon to start operating in Malta.
Easyjet are soon starting, and probably Ryanair in the near future. with the exorbitant ticket prices charged by Air Malta, one wouldn't be surprised if the airline is forced to take some drastic measures soon.
and yes, KM pilots are arguably some of the lowest payed in the EU.
the problem is that, Air Malta being the only airline based in Malta (apart from Britishjet, which owns one MD-90), then there isn't much of a choice for pilots wishing to live in Malta. they either accept the low wages or drag their families to go and live in another country. and since Malta has no land links to mainland europe, then travelling to and from is quite expensive. not to mention the high departure tax charged by Malta International Airport. Pity isn't it?