There is is a difference between being malicious and being gentle. The Klingons aren't gentle. To even compare the Federation in this to the Klingon Empire, is disingenuous at best.
Because the alternative is that the Federation collapses, in total, and the Klingons colonize the now vacated worlds that were once populated. In other words what some here are advocating is self extinction...
Is the Federation perfect? No!
Are the Klingons perfect? About as far from prefect as it is possible to get.
This is one of the major problems with a small universe
In other words we haven't seen the Federation as of yet. Small universe, remember?
The Federation is an idealized version of the United States. Keep in mind that in the 1960s, there was still a great deal of work to be done. The Federation had far less work to do.