Hurting would assume some kind of degradation of the genetic code resulting in either :
A less healthy plant, less able to survive, grow, or propogate
A less desireable plant, less capable of serving our wants
So with all the inbreeding of narcotic cannabis, you could say breeders are hurting, as they are attemting to homogenize the genotype of their strain, lowering genetic diversity an ultimately creating monocultures of homozygous genotypes, lowering the probability of mutations and inevitably hurting the plant's chances outside of the controlled environment.
Or, you could say they are hurting the gene pool by focuing on increasing THC content, juxtaposed to other traits and cannabanoids that may inevitably be linked to other, sometimes more pleasurable effects of consumption.
Or, no of course they aren't, they've taken weak, hermie sativas and converted them into juicy, fruity, stable strains, phenotypically similar or identical for an increased commercial viability and customer satisfaction.
Or, no they aren't because it's a gene pool, and thinking of it as getting "hurt" or "helped" is purely subjective and has many independent variables, componded by the exponential facets of genetics...it's impossible to hurt or help a gene pool, only can one change it.