So, this is more of an archaeological question as the inhabitants of Malta didn't leave any written records.

The temple-building culture had a fascination with life (fertility, sexual imagery) and death. It is no doubt that fertility rituals occurred, and that the were a significant component of the religion This can be seen in various artwork that have been found depicted fertility or sexual imagery (ex: fatlady/venus statues, phallic statues). Also, architectural features of various temples such as the orientation towards the rising sun.

However, it seems that there were also significant emphasis placed on death, with death rituals occurring. This has been found while excavating large burial complexes such as the Hal-Saflieni Hypogeum and Brochdorff Circle in Gozo.

Maltese temple culture flourished roughly from approx 3600BC to 2500BC. During this period, temple construction gradually became more elaborate and colossal. By 2500BC, it seems that vast energy and effort was put into the building and maintaining of these structures (along with religious feasts and rituals) with little attention given to the building of villages and domestic structures.

Religious and cult influence resulting in social control of the population seems to have been significant. As Malone et al state (1993) states:

Cult activities seem to have reached a feverish pitch in the final phases of the Tarxien period around 2500 B.C.E. The society was becoming increasingly dominated by a religious hierarchy in which cult specialists or priests controlled much of the industry of the people.

The fact that any imported materials from Sicily is often found secreted away in inner recesses of temples and mortuaries also seems to indicate that knowledge and contact with other cultures was restricted to the priest caste.

Malta was going through environmental change around 2500BC (the height of the temple phase), which was likely due to environmental degradation (deforestation leading to soil erosion, poor agricultural practices). By 2000BC the culture vanished and was replaced with one favoring cremation. Interestingly enough, it seems as if the temple builders literally disappeared. No single element of this new culture can be traced to the previous ones. (Trump, 2002). For example, apart from cremation, the pottery is different style and this new culture used copper tools.

It could be that also internal conflict hastened this decline. It has been theorized that due to the large amount of temples for such a small territory, it could be there there were a handful of rival tribes vying for control.

Sources:

Malone, C., Bonanno, A., Gouder, T., Stoddart, S., & Trump, D. (1993). The death cults of prehistoric Malta. Scientific American, 269(6), 110-117. (Updated version here)

Trump, D. H. (2002). Malta: Prehistory and Temples.

Newspaper article/interview 2014: The Death of the Temple People