I guess since 91.117(d) is clearly specified in that Docket No. 24456; Amendment No. 91-233, as you have provided, and since 91.117(d) clearly covers *any* "operation", as defined before, and ATC in itself must NOT and can NOT be considered an "operation", since, according to FAR 1.1 it is only a service "operated" by approprate authority, you are right. Clearly, the act of "operating" or causing to be "operated" the service of Air Traffic Control by persons cannot be considered in itself to result in "an operation" of that service, so 91.117(d)..*any* operation..., is unequivocally included in Docket No. 24456; Amendment No. 91-233, which prevents that operation of the service of Air Traffic Control from being considered by definition "an operation".
And 91.117(d) clearly states only the pilot may determine the "minimum safe speed" for *any* "particular operation", and allows only the pilot to define and interpret 91.117(d), "..particular operation...", according to his and only his need, for what is granted by the authority of 91.117(d).