I think the indoctrination concern is a bit unfounded, my understanding of the choice to study the station was more literal than it seems many believe it is. The human reaper is (hopefully) largely destroyed, and thanks to its being at a very early stage in development, its destruction should have very reduced indoctrination effects, if any. Additionally the reaper was classified as both synthetic and organic, so the radiation could have inflicted even more damage upon the baby reaper than is shown in game. However study of that destroyed reaper is secondary compared to the research I was considering in this situation. The base is Collector by nature, not reaper. The Collectors are mutated Protheans, molded by the reapers yes, but not in any way directly related or similar to the reapers. The reapers (more likely individual reaper, who my guess is names Harbinger, and was just speaking through the collectors) controlled the Protheans, but they also released this control at the end of the game, shown quite clearly. I see little to no reason why studying the collector ship would have any more chance of indoctrination than studying Ilos, or any Prothean ruin would. The discovery on Mars that brought humanity into the galactic scene was also Prothean tech, likewise the beacons, etc.
The Reapers used the indoctrinated Protheans to help wipe out intelligent life in the previous cycle. It is likely these Protheans who became the collectors, and the only imaginable reason the Reapers left them alive was a type of safeguard should Sovereign fail. Because they were effectively a backup plan, it makes sense to keep them somewhere safe, logically the Omega 4 relay. The Reapers wouldn't have need for a full race or army of Collectors, explaining why there is only 1 ship, and 1 base, rather than a full civilization spread across multiple planets with many ships. The Reapers likewise would have little reason to develop the Collectors tech all that much, they were used as basic cleanup tools, they don't need significantly advanced tech to do this. It appears there is reaper technology at work with the collectors, but it is very difficult to determine what is specifically Reaper tech compared to standard Prothean tech. Protheans were capable of creating a functional mass relay of their own, its not unlikely that their beam cannon and majority of advanced ship tech was also theirs. A wide sweeping rant, but overall point is researching the base is not just researching another dead Reaper, its a very, very different situation.
While dispelling ridiculous ideas about why its renegade to study the tech, there is no way the ship would be used to build a new human Reaper. The number of humans needed, uncertainty about allegiance, and overall lack of understanding about details of the process all suggest this would never happen. Surely Shepard and others would stop TIM from going that far as well. However you can learn a lot about how to break something by looking at its blueprints.
While research teams are unlikely to be indoctrinated (imo), it is very possible that the few reaper techs on the collector ship would require a lot of work to understand or even just use. The Reapers set up the relays and the Citadel on purpose, they are supposed to be user friendly. The Collector base was not part of the guided development trap, and would not need to be well understood by the Collectors or anyone else who stumbles across it. However flip side is the Reapers wouldn't likely put the same security measures in to hide their presence or retain control of it. Saving the base could still result in nothing though, if the technology is so advanced and divergent that it is still worthless by the time the Reapers arrive. This would be an effective way for Bioware to keep branching storylines reigned together, but its also a cheap way out of the situation.
The way I ultimately approached this and other obviously large decisions in ME2 was similar Jonny_Evil, except I had little fear of indoctrination issues. Overwrote the Geth, kept the genophage research, anything that could develop into troops or resources later was the right choice. Maybe this will result in an easy mode ME3 for my character, hopefully not, hopefully the Reapers are as big a threat as they are portrayed, but only time will tell.
I write too much
-TrueRedemption
P.S. Jonny_Evil, sacrificing a ton of lives to ensure the safety of the galaxy sounds more like development of the clone army rather than just the Emperor =P
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