Depends on the structure, imo.
There's a particular Blooder exploration site I run into frequently that drops a bunch of slaves, slavers and hounds when you destroy the structure that is one of the two escalation triggers. (The escalation itself has at least one mission that does this again, where either a faction rat or a large structure is the trigger for the escalation.)
Said structure has a lot of HP and takes nearly a full reload's worth of HM fury missiles from my Tengu to chew through - plenty of time for there to be warning for people to get to escape mechanisms and whatnot. If it were a much smaller/weaker structure that only like, took one shot to blow up? Probably not something I could justify doing much of anything with, myself.
Since I have to blow the thing up to get the escalation, what I typically have done is handwave a rescue operation with boarding parties sent in while I'm clearing tackle and neuting rats from the field; once those rats are off the field and I focus on the structure, the boarding teams return with rescued prisoners (slaves), apprehended Blooder overseers (slavers) and hounds - the numbers of each that are dropped in the can when the structure is destroyed I consider to be the number that either weren't killed by the Blooders in a scorched-earth policy (the slaves), or couldn't escape the boarding teams (the slavers).
So I'm kind of inverting the order of gameplay (recovering people before the can spawns) and the literal identity of some of the livestock items for RP purposes (since, really, 'slavers' in a Blooder facility are going to be Blooders, the slaves are going to be kidnapping victims whether or not they were slaves beforehand).
As for the destruction of the structure, I consider it a denial of assets. By destroying it 'after' I've rescued people from it I prevent it from being used again, provide a little bit of closure to those rescued, and of course snuff out a number of heretics all at the same time.
As for what I do with those people:
- After I'd collected a nice large batch of hounds, Morwen donated them to Istvaan, who had a place for them (got some fun RP out of that one, thanks Istvaan ♥) to be fed and taken care of.
- Slavers (aka overseers/Blooder crew) go into a special quarantine area. I handed off about 250 of them to Aldrith at one point during the KotMC 2.0 era for him to 'deal with'. Coming up on about that many now and need something to do with them, actually...
- The slaves (aka, rescued people that may or may not have been slaves to begin with) are provided housing, medical care and other amenities. I've tried starting some little RP arcs to get them sent 'home' but the last one or two I attempted kinda fell flat when people on both sides stopped responding to mail. In the meantime, those who were able to work (presumably most of them) have been given temporary stationside employment in TYRIN facilities for some spending money and to keep them doing something, since activity is healthy.
Aside from these I usually ignore structures that aren't required for progression.
Except Sansha ones.
Those can die in a fire. Repeatedly.