I've always taken "indoctrinated" to mean more forced. For example, sometimes people indoctrinate their kids with their religious or political views. "Assimilate" sounds like he was integrated into the new organization more naturally. Sort of like "immigrants assimilated into their new society."
I agree that there is a "bad vibe" or negative association attached to indoctrinate, it can bring to mind images of forced teaching or brainwashing.
However, here is an example which I hope will demonstrate that the word can be used in a positive way.
All the new employees attend a short orientation lecture which explains the companies values and the procedures that are followed to accomplish typical tasks. Everyone appreciates how this indoctrination helps them to assimilate into the organisation.