I read it is unethical to hire someone because it breaks the second categorical imperative which is to treat people as an ends. If by hiring someone to do something you are treating them as a means to get a job done and therefore it is unethical. Are there any counters to this?

You're missing an important word. The second formulation of the categorical imperative in the Groundwork is:

Act in such a way that you always treat humanity, whether in your own person or in the person of any other, never simply as a means, but always at the same time as an end.

The key phrase here is "never simply." Kant has no problem with entering into mutually beneficial rational contracts.

Maybe stated in another way, using someone as a mere means is abusing their rationality by getting them to act in a way inconsistent with how they would act when fully informed.

In fact in the Metaphysics of Morals, this is how Kant understands sex and marriage, because Kant views sex as using another person as the means to your gratification, and he thinks this is only justifiable insofar as you both rationally consent to the arrangement -- and make it permanent.

For instance, Kant sees it as an abuse of a ticket seller to pay with a credit card you know is stolen. Or conversely, to sell seats you know you don't have the rights to.

For Kant, employment itself should be a rationally entered into arrangement between the employer and employee where they understand what they agree to.

References

http://www.utm.edu/staff/jfieser/class/300/categorical.htm
http://alexanderpruss.com/145/KantOnMarriage.html

See Also

Kant's second formulation