I am going to take a diversion from the letter of the question, because the context cannot be ignored here - if you plan to use this in the context of team management you should not use words with too-negative a connotation: this would simply instill unease in the people who are not the "rotten fruit".
And therein lies a problem: the use of "rotten fruit" when talking about your team. Team management techniques are of course outside the remits of this forum, but this leads me to the word I am getting at:
Pruning is the action of removing dead or overgrown branches from a plant (https://en.oxforddictionaries.com/definition/prune#h46946740871680, meaning 2). This provides a better mental image: the team is seen as a tree, growing upwards, the problem team members are removed due to a natural progression, and the same expression can be used with less negative connotations for the individuals if the team is pruned due to restructuring etc. Additionally, this expression is widely used in team management, so it will make immediate sense to upper management.
The above remains within the realm of fruits/plants; an alternative could be jettison (https://dictionary.cambridge.org/dictionary/english/jettison), but pruning is, as I said, a better mental image.