Using Alert(Purge) score deduction would solve the problem (no point score farming through wanton destruction if you're not actually getting a score benefit), but it uses a meta, non in-game mechanism to alter gameplay behavior.
That's an interesting conclusion, certainly different from what I was thinking. My intent was to adjust score in a way that purely reflects the difficulty created by your choices, while here I believe (?) you're assuming the player's goal is to maximize their score. I personally don't care about score other than as a fair reflection of how challenging the run was, so it wouldn't bother me, but I can see that change rubbing some players the wrong way, those who go for score. That said, the latter category of players could already be irked by the fact that stealth runs are inherently low scoring...
One, wholesale destruction of machinery eventually raises the Alert level to an extent that outpaces purges.
The main issue I see with this option is balance, because a
really good hacker can theoretically always purge all alerts.
I do like the idea of greater implications for machine destruction, though this topic extends beyond just machines to robots, which are where the points really lie. You can theoretically get the AI to call in a large number of squads, if you think you can handle them, and mow them all down for points. Machines aren't repairable, anyway, but there is an endless supply of robots.
Another alternative would be to limit the number or combined effect of your purges. Maybe each time you do it on the same floor it becomes less effective (which could be explained logically in a number of ways).
Farming is solved in some other roguelikes via out-of-depth encounters, though we don't necessarily want to tie that to a specific number of turns like in DCSS. Something bigger/nastier
could show up, but it would have to have a good reason... perhaps what Reiver suggests below
Solution 2, give level wide consequences to the destruction of things like reactors. Currently, the player cares about terminals, scanalyzers, repair stations, etc. The player doesn't really care about reactors or the like, except to the extent that you want to take care to no get caught in their blast radius, and sometimes want to blow them up from afar to take out enemies. But surely those neutriono reactors, etc are serving some purpose for the complex. What if destroying certain structures had a chance to make nearby Terminals and so forth shut down? the flavor explanation is that the terminal is depowered without the reactor. If there was no guarantee that there would be a functioning terminal around for a purge, that would thoroughly disincentivize blowing the crap out of everything.
This. It could also add to the verisimilitude of the whole setup; wonton destruction results in harming the base in meaningful ways. Of course, the more critical the component, the more valuable the score... 
I do like the way that goes both ways, like so many other aspects of the game.
Alternative: Purging alerts is also tracked. Too many, too reguarly (aka dozens of times on a single level, a key to farming in relative safety) starts risking triggering a 'sysadmin' response from [EXPUNGED]. This response is not gentle. The difference between getting caught by automatic security systems, and something going "Wait, that activity looks a little funny... OH CRAP I've been hacked for the past three hours BURN EVERYTHING"
This sounds both very mean and very fun at the same time
Maybe a combination of this and the diminishing returns.
