Answer: An ideal Objectivist society would be one where there would be maximum individual freedom, and minimum governmental functions, primary among which would be preventing the infringement of individual rights. Such a society would allow for the formal formation of any private groups with common interests as long as they abide by the essential rule of civilized society - non violence. If a set of peaceful people (including workers) comes together for any legal reason, then yes, they are completely free to do so. A union in this sense is no different from any other group of citizens that chooses to organize itself into a formal association. In fact, if the formation of labor unions were illegal, this would violate the fundamental human right to freedom of association.
Although labor unions have been historically associated with violent action plans (non-peaceable strikes, rioting, picketing etc), this does not mean that all labor unions will necessarily be violent. Workers can have legitimate demands that can be lawfully stated. The employer can accept, reject or negotiate these as he sees fit in a society that values individual rights because he faces no personal threats or compulsions. He is protected from the potential use of force by the law.
Unionization of firms as it occurs today is usually a process that works by majority vote and thereby ignores the desires of individual dissenting workers. In the ideal Objectivist society, this forced unionization of workers who may not want to be part of the union would never be allowed as it violates the rights of those workers. In addition, there would be no governmental interference in unionization or in their formalization. Labor unions would be private and voluntary groups of workers, dealing with employers without unnecessary governmental regulations.
Labor unions that succeed in achieving their values are not doing something morally wrong. The workers are free to make their demands in any way they chose, including collectively. They are free to chose to express their demands as a group and with the condition that negotiations include all members. The employer is not forced to give in to these demands if he considers them unreasonable. Thus this "achievement of values" is not by pull because it is a not an achievement tainted by illegal or illegitimate means. It is a "value" that has been obtained with no use (or threat of use) of force on either side.