If I send a force to investigate a missing squad, do I get gene seed?
Assuming you find a body, my answer would be yes. Of course, in most circumstances, why would they leave a body around for you to find? So I think it'd depend on the context.
My biggest complaint about Duke's Chapter Master is that it is so swingy.
You either crushed everything leading to no deaths and no gene seed OR every dies and nobody lives to collect the gene seed.
I'm definitely thinking about this as part of the strategic layer. My current design thinking for this iteration is that planetary invasion looks something like this:
Stage 1: Planetfall, complete with drop pods, to form an airhead/lodgment.
Stage 2: Player has two sliders: one that's wall->spearhead for defining how concentrated your forces are, and one from "Make them pay for every inch you give" to "push them back at all costs".
As your forces expand from their initial lodgment, protecting their gains will require spreading thinner, making them more vulnerable, and while pushing aggressively forward might be able to wrest control of the planet faster, it'll almost certainly come with more casualties. Whereas taking some time to thin out the enemy forces in advantageous engagements can make future advances far less risky.
Your point does have me thinking about whether I should implement some form of "leave no man behind" when I start working on retreats... of course, once I actually implement apothecaries properly, that won't be quite as necessary (though leaving behind a mostly intact suit of power armor still just seems wasteful).
Unfortunately, lore-wise gene seed is only pure if obtained off someone you see die.
Otherwise Chaos invariably corrupts the gene seed the very second it leaves your sight.
I have been idly contemplating how I want to handle the concept of gene seed taint down the road. My initial inclination is for mutation, if I want to include it, to be a pretty slow, subtle thing, and certainly not as drastic as you describe.
What if instead of finding a dead squad, the player finds a small band of survivors? Scout Marines are trained to survive if they are outnumbered and outgunned rather than needlessly confront and die. Their job is to report back if able, or hide until friendlies arrive so they can share intel.
I may change my mind later, but I think the way I'd handle this scenario is that it'd just be a battle with survivors... I'm currently hand-waving all squads having the technology to communicate with you within the week that a turn represents, so I'm not currently building in a situation where a force would "go dark" and have to be searched for and found alive later. I'll consider it, though... though the idea of anyone taking a Space Marine prisoner seems like such a bad idea...