The Institute's decade after decade of compounding crime against humanity on top of crime against humanity works both against them, even if you have a reform oriented director, and against the Railroad.
It will take decades, let alone years, to unravel that sort of mistrust and suspicion, and lots and lots and lots of showings of altruism and sincerity (part of the whole reason Deacon is like 'we gotta help regular people more' -- he recognizes this).
And even then... for some, there will always be hate (not undeservedly in this situation).