Ultimately, I think this particular debate is somewhat pointless because when the script loads up whether from chapter #1 or later on. Because typically variables are not always set at the start of a script, but usually they are 'sanitized' to prevent variable corruption down the road as the script performs.
So the STD variable could very well be already set from the get go as "false" until you sack Air head Arieth (I don't even know if that's even possible in the game as I just never liked that twat, so even if she was a possible LI, I still wouldn't touch her with a mile long pole).
And if Arieth is accessible then it's not much to add a line at the end of that hypothetical Arieth encounter like
$STD_clean = "False";
And that's the only extra code required to make that happen. and if you wanted to get creative you can even create a condition of getting treated for it
If ($STD_clean = "false" && $STD_treatment ="false")
then ($MC_LOSES_ALL_TEETH_AND_GROW_THIRD_ARM_AND_3_NOSES = "true");
and end up with all sorts of hilarity
Point is, programing-wise this isn't much to add to the code to make happen, where it gets complicated is with the scenes and renders. that's mostly where the heavy game work rests.