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After all the time that had passed and money spent it would be hard to justify the project if Accelerator just up and left. It would be nearly impossible for them to justify starting all over with a new subject and all the data gathered from Accelerator would have been labeled useless if they switched to another subject. Not to mention all the money and time wasted on him and the clones. Accelerator participating was an important part of the project, had he left after the killings started they would be hard pressed to start up again and would have to redo all the calculations for another subject that wouldn't be able to bring what Accelerator could.
I do agree that Accelerator purposely tricked himself to believing the killings weren't wrong because of how the clones acted and how illogical it was that they all embraced their deaths without a second thought. Like dolls. Hence why he regrets what happened because he knew that he was only fooling himself and deep down knew it was wrong but didn't stop it.
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