The crew were joking about the scenario, but they at no point allowed more photonic lifeforms to die for their entertainment. Remember like half the Voyager crew died in the first episode. It's kind of like how a surgeon can lose a patient then immediately go joke around with their buddies, when you've seen a lot of people die you stop letting it affect your demeanor.
And you simply can't do a parody of black and white B-scifi without making it humorous.
Of course. But then they should have said the failsafes are affecting the photonic lifeforms also and are storing them in some buffer...or...something.
So many Voyager eps could be improved with the slightest of handwaves.
Also re: Bride of Chaotica, a little more meta-humor would have been nice. At one point they go directly from the holo-deck drama to the Voyager problem with "We're slipping deeper into subspace!! (cue dramatic music)...it's a weird moment. You're thinking, "Wait. are they doing that on purpose?"
Throw in a few lines maybe like, "It's always something. anomalies, aliens...come on...what's next? Giant Space Ameoba?"