At the time, it was concluded that yes, a high tail would cause pitch up. But the addition of a low tail on the F-104 was determined to lead to longitudinal and directional instability, increased drag and overall decreased combat utility, meaning maneuverability.
The F-101 was essentially subject to the same imagined deficiencies when it was designed. The XF
-88 (from which the design of the -101 was taken) had a tail lower on the vertical, and I can't think of any reason why the tail position was changed other than the same reasons Lockheed used the high tail on the F-104. The -101 was a big airplane, and to make it more maneuverable, a high-mounted tail was the best way. The known problems with pitch-up were to be ironed out as the airplane went through Category I flight testing, and fitted to the production airplanes. However, McDonnell never really solved this problem.