The word "referendum" is vague in English, but it's the only term for the least-binding question a government can ask of its citizens. I am not familiar with the Spanish system of autonomies, but in federal systems like the US, small bodies regularly pass referendums, resolutions, and even laws concerning how they will interact with larger ones. Usually without such direct violence, even when the laws conflict.

On a purely practical level, by cracking down on the vote, they only ensure its outcome. See if it passes and then strike down the resulting legal structure in a higher court, at the very least. The constitution of every divided country has measures to deal with these, and the first step is never "cracking skulls."