Shandepared wrote...
Yes and
this is true if you rewrite them too. Regardless a minority will be left
in isolated systems. However even if they do rebuild it will take "many
years".
Very much so, and during that rebuilding phase, if you destroy the Geth Heretic base, they wont be a threat to Galactic Stability, while if you re-write them, there's no guarantee that the re-writing will stick. IMO, regardless of the moral side of re-writing a possible evolutionary stage in a species life cycle, you run the risk of either re-creating the heretic faction, or causing what you were hoping to avoid, that being the Geth breaking their self imposed isolation and charging across the galaxy to exterminate organic life.
Shandepared wrote...
Then humor me and tell me how you'd justify letting the rachni go as a renegade action and killing her as a paragon action.
Sure, I'm willing to take a stab at it.
Paragon - The Rachni have proven to be a serious threat in the past, to the point where the citadel races were forced to exterminate them as a species. While some disagreed with the decision, the end of the Rachni threat was a good thing for the Galaxy. Now, a rogue Genetics company, in league with Saren, a known threat to the galaxy has been caught in the act of recreating the Rachni. Who knows what genetic changes they have done to the Queen, have they increased her intelligence, her guile, have they increased the strength of the Rachni, turned them into even more dangerous, feral animals than they were before? Are they even Rachni anymore? Can you take the risk to find out?
The Rachni Queen is not in a position where she can escape or attack Shepard, the only way she can preserve her life at this point is to beg for it, promise anything to ensure her survival so her brood can repopulate. How likely is it that she'll keep her word? You cannot know. What you do know is that the Rachni Queen represents an immediate threat to the galactic community you've sworn to protect, and right now, with the threat of Saren and the reapers, the galaxy can't afford another unstabilizing component. Though the decision is distasteful, you use the failsafe to dispose of the Rachni Queen.

Renegade - The Rachni Queen is helpless, begging for her life, she's promising you anything to ensure her survival. Your hand hovers over the failsafe, but wait you think, the Rachni were a serious threat once, long ago, the Council Races uplifted the krogan to deal with them and the Rachni fought to the last egg. Perhaps they could be useful... What changes have the Genetics company made? Perhaps the Queen is more docile, while the drones more powerful and aggressive, the drones you fought on your way here certainly gave you a hard fight.
Maybe if you show a little "Mercy" to the Queen now, it'll pay off down the road. A bunch of angry bugs to use as cannon fodder against the Reapers might be helpful, and you know, if one of the other council races get out of line, the fear of the Rachni might convince them to behave... Get them focused on the real threat instead of ****ing in your ear... You talk with the Queen, getting her to swear her loyalty to you before you release her, a loyalty you plan on enforcing under the threat of your gun.

There you go, a paragon reason for killing the queen, and a Renegade option for releasing her. Not what's available in game, but options that certain types of Shepards would think of.