So, how do we go after these guys then?
That's been studied at length. And the solution is "simple", i.e. easy to state but harder to accomplish.
Terrorist organisations (from a military standpoint) rely exclusively on the civilian society for support. It's their logistics, intelligence, funding, base of operations etc. etc. So, what you need to do it distance the organisation from its support for long enough that it starves and dies. This can be done the "nice" way, like the British in Burma, whereby they armed the local population and worked with education and propaganda to isolate the communist guerilla. But you don't have to be nice as demonstrated in Kenya with the Mau Mau where strategic villages (aka "concentration camps") effectively isolated the guerilla from their support. The organisation that ultimately won was the same in name only, and it was mostly political pressure from abroad on the government that made them abandon their largely successful approach.
The other thing you have to remember is that to win takes stamina (something the US has always lacked abroad). The guerilla only have to not lose to win. As long as they exist and can perform operations they're in business. The other side on the other hand has to actually win, i.e. defeat the guerilla in detail, so that they virtually cease to exist, in order to claim victory.
Given this, there's little to support a campaign of drone strikes. It's very difficult to see what such a campaign would ultimately achieve other than as a small part of a larger strategy.
There was an article in Parameters, Scholarly quarterly journal of the US Army War College a few years back on this very topic. So it's not exactly new knowledge. If you leaf through that they often have papers on irregular warfare (not surprisingly). It's available for free online.