No clear-cut distinction can be drawn between professional and amateurs in science: exceptions can be found to any rule. Nevertheless, the word "amateur" does carry a connotation that person concerned is not fully integrated into the scientific community and, in particular, may not share its values.
Nor, if regularity and conformity to a standard pattern are as desirable to the scientist as the writing of his papers would appear to reflect, is management to be blamed for discriminating against the "odd balls" among researchers in favor of more conventional thinkers who "work well with the team."