No squint-eyed pixel hunting + puzzles that are common sense and objective enough = WIN.
SPOILER ALERT BEWARE
Just a few plot-related comments...
I think that blowing yourself up in the lab with BOTH of the crystals (i.e. the one you cough up along with the one in space) should count as a "The Truth + Decontamination + Hull Breach" ending.
I also think that if you use the escape pod after learning that you have been infected, it warrants a special medal.
It would have a been a nice touch to have the option to eject the data log in space or something, so that if you blow up the entire ship, it is an alternate way to achieve "The Truth + Decontamination + Hull Breach".
I get the impression that destroying all evidence is the canon ending, though; I mean, if you have family, you definitely would NOT want them to find out about your spree-suicide (nevermind the influence of the crystal), especially if it would affect condolence pay going towards your family; I completely understand why "destroy all evidence" is canon in that regard.
Speaking of crystals growing in people, I wonder which came first- Primal Sands or SCP-409?