[Archonsod]

The value is always relative. First thing to ask yourself is whether you have anything else to be spending those nature gems on.
Secondly, how long are you likely to be without a pearl income? Empowering for the clams is going to be a long term thing (if you gain pearl generating sites you'll have a higher astral income of course), while in the short term it would be cheaper (purely from a gem expenditure perspective) to use alchemy to cover emergencies.

In other words, if you're looking for a cheap short term solution then use alchemy if you need pearls, and concentrate on taking back that site. If you want a higher pearl income, and you don't mind waiting a while for the payoff, then empower.