You want one of these: Even though in the beginning she was ruthless, she soon became a better person. Even though, in the beginning, she was ruthless, she soon became a better person. I much prefer the first.
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You want one of these:
Even though in the beginning she was ruthless, she soon became a better person.
Even though, in the beginning, she was ruthless, she soon became a better person.
I much prefer the first.
There is no version in which a comma after 'in' would be correct.
Are you confusing 'before' and 'after'?
CJ