Note that it's usual that companies gets tax on surplus, not income. So we are already 'punishing' the efficient ones, we are just doing it in a relatively neutral way.

In systems with progressive income tax, the total tax income from a company with 1 employee making X$ is more than if the company had 2 employees making X/2$, so essentially 'punishing' using highly skilled labour over more less skilled ones.

There are no perfect taxes, and current tax systems have adapted from a lot of practical concerns. Some of those is that's it's easier to tax money as they are moving around vs when they are sitting still (wealth or property tax), and it's easier to tax people than abstract entities like companies, since people have a harder time moving. And for the same reason, it's easier to tax the middle class than the owner class, since the richer you are the easier it is to move yourself and those you care about to wherever taxes are low these days.

All these practical concerns have made it such one of the most common ways for the state to get a share of the productivity of its society, is from income tax. But this is not a 'economic law' that if must be like that. If more and more of the productivity and wealth creation in society is produced such that there is little employment income involved, we will have to find other ways to tax it.