Was destruction of SR-71-related tools really extraordinary?
was there any legitimate reason for it?

Unused tools, the tools for making a plane which isn't made anymore, are most probably put somewhere in storage, since the factory floor is best used for actual production.

While an aircraft plant for making top-notch, spyplanes is generally quite secure, any storage facility is probably less secured. Maintaining a high-security level for a storage facility seems like spending good money for a not awfully good purpose.

So in order to prevent the tools for the secret planes being stolen from a run-of-the-mill storage facility, it is much more secure to have them dismantled.

Note, that the SR-71 was produced in a time, where 24/7 surveilance was not as common as it is today. I suspect, that setting up a high-security storage facility would involve a lot of guards guarding basically junk-metal. Guarding scrap metal also doesn't seem to be an awfully motivating task for the guards.