Yes it is. The but is necessary because the second part of the sentence is not a clause--it doesn't stand alone as a proposition. The rather itself approaches redundancy, but it does intensify contrast. In order to lose the but, the sentence needs to do something like this:
...not a diplomatic measure to intimidate the Soviet Union; rather, it was a military measure...
It might help to imagine a clunky pair of commas before and after the rather. Note nevertheless how little is lost by dropping the rather altogether.