Another issue might be testing EMP against an active part of your nuclear deterrent, with a potential risk of damage to the Launch Control Center (LCC).

The Echo flight LCC was probably connected to miles of highly conductive communications cables, both to its 10 Minuteman 1 silos and its Squadron Command Post (SPC)- fibreoptic comms links were in their infancy in 1967

External Quote:

Wikipedia, https://en.wikipedia.org/wiki/Optical_fiber

An argument could be made that the best "specimen" for a test of this sort is the missile system as actually deployed, but this seems a risky strategy considering that, by definition, the amount of damage done (if any) could not be accurately predicted- this, after all, would be the point of the hypothetical test.

Even if a portable EMP generator existed in 1967 (which seems unlikely reading @Mick West's post), and even if it was used to test the "hardness" of Echo flight, not advising the LCC or its Squadron Command Post, or the above-ground security troops, seems an absurd risk to take.
It could subvert the confidence that the men had in their equipment and in their own physical safety, with consequences for morale.
All that would be needed would be to brief the very small number of personnel in the LCC and its SCP that shift something along the lines of
"Our scientists are developing a way to disable Russian missiles by interfering with their electronics. To test their theories, they're going to run a small-scale experiment to see if it disrupts our systems, so there might be some disruption starting from ------ . There is no risk to yourselves, it's an electronics thing. This is secret; don't discuss this with the other flights, who are not involved, or with anyone else. Please go about your duties as you normally would this shift."

The LLC officers would be (hopefully!) trustworthy and reliable men, a briefing like the above gives away very little.

Similarly, not briefing the security troops that a big glowing thing was going to be hoisted up from a truck (or whatever) in the immediate vicinity of the LCC compound seems risky; they were defending a nuclear missile launch facility.

Robert Salas claimed,

External Quote:

Jim Klotz, Robert Salas, 27 November 1996, The Malmstrom AFB UFO/Missile Incident
(https://www.nicap.org/reports/malmstrom67-2.htm, appears to be a NICAP webpage).

-In the circumstances, with a man injured (how?) by the glowing thing, it might be surprising that the guards didn't seek permission to fire- or even just open fire (depending on their rules of engagement). They're at an isolated nuclear missile firing post, and they're under attack!
Not that I'm particularly won over by Salas' description of events.

Not directly connected, apart from demonstrating the scale of equipment needed to assess EMP effects on military equipment over 50 years ago:
ATLAS, Air Force Weapons Laboratory Transmission-Line Aircraft Simulator, started construction in 1972.
The enormous wooden structure, "the Trestle", was built with wood, glue and fibreglass pegs:

External Quote:

Mental Floss website, "The Largest Wooden Structure in New Mexico (And the World)", 08 December 2014, Rob Lammle
https://www.mentalfloss.com/article...largest-wooden-structure-new-mexico-and-world

(Not sure about the "teardrop" bit, but there you go.)