Gray Morality

I don't understand how keeping the data earns renegade points while destroying the data earns paragon.  I mean I know how the data was obtained in inhumane ways--but that's why with it in Mordin's posession vs. Maelyn's--something good could actually come out of it.  Heck, if I was one of the people experimented on or even killed by the experiments, I would have preferred my sacrifice not be in vain.  I would have wanted something good to come out of it.

While I understand that y'know that data was obtained via inhumane experiments and it might tempt the researchers to blur the lines a little--if someone like Mordin was working on it, I tend to doubt that would happen.  He could have helped cure the genophage and it nets renegade points?

My Shepard stated straight up (and I agree) "I would never consider brainwashing an organic race, I'm not about to consider it for synthetics."  That's mighty paraphrased, but the general gist is there.  Look, the Heretic Geth will not follow logic, they are fundamentally flawed at the most basic level.  We cannot convince them (which would be the most civilized option) which leaves two options.  Either destroy them, or rewrite them. 
 
Quite frankly both of these decisions suck, but honestly, the can of worms that rewriting the Geth opens up is way too huge.  WAY too huge.  While I might not like the idea of killing so many Geth, it's mainly because they're not active combatants, that entire station would have eventually been mobilized with the Reapers and against the Normandy and Citadel space.  The second option though, is just reprehensible.  Rewriting any being's fundamental core is wrong on every level.  Especially because we don't know exactly how it would have worked out.  What if the Geth were aware of what they were before, even if it didn't cause anger or rebellion, it would still cause some form of stress, depression, or dissociation. 
 
Long story short:  If I kill them, they die as they chose to live.  If I reprogram them I decide to be the arbiter that chooses what is acceptable or not.  So it's kind of dumb that destroying said Geth base gives renegade points.  Like seriously wat.

Yes, it was a horrible facility, yes, it was an inhumane and monstrous place--no arguments there.  In fact I fully support the fact that my Shepard blew the place to heck--however were it not for the fact that I knew the Illusive Man was indoctrinated I would be far more hesitant.
 
That facility was creating a Reaper.  What if through study of it we were able to replicate or even defend against their weapons?  What if we were able to find a viable solution aside from organic/synthetic tissue to construct their carapace from?  What if the entire universe was able to band together to essentially create our own Reaper--devoid of the horrific sacrifice that the Reapers intrinsically desire?
 
It would require strict supervision, naturally, heck it would require multiple levels of observation to ensure that everything stayed on the up and up and there were no inhumane experiments being continued there.  But think of the advantages that the entire universe could have gained from keeping that facility intact.  The only two reasons I can think of that this would be bad are
A: The Illusive Man being so obviously indoctrinated
B: The fact that an incomplete Reaper was inside it.  Who knows if an incomplete Reaper is still able to indoctrinate people in the facility.