The reason they decided to do so is that the name “Ju-Che” has always been polemic as it is the word used by North Korea to describe their ideology. There used to be another pattern in the Chang-Hong set called Kodang; however, Gen. Choi announced that there are some extra techniques he wanted to be part of the twenty-four pattern set and therefore replaced Kodang with this new one called Juche. Many people are agreed that Kodang was replaced with Juche to appease North-Korea when Gen. Choi went there to introduce Taekwon-Do (and get financial backing) in the early eighties. It is believed that replacing Kodang with Juche was a political move. (A must-read book on the politics of Taekwon-Do is 
Alex Gillis' A Killing Art: The Untold History of Tae Kwon Do
.)
The pattern Kodang was named after an independence movement activist Cho Man-sik 조만식; his pen-name was “Go-Dang” 고당. Cho Man-sik was basically the first president of North-Korea (“Chairman of the Provisional People's Committee for the Five Provinces”), but was ousted by the Soviet forces who instated Kim Il-sung, the “father” of North-Korea. Cho Man-sik and Kim Il-sung did not see eye to eye so Cho Man-sik was put under house-arrest. He continued to speak against Soviet-Communism including Kim Il-sung and was eventually silenced. He was sent to jail where he disappeared. Many are of the opinion that Kim Il-sung had him executed. A large number of people who prefer Cho Man-sik's penname “Kodang” over the name “Juche” often state as their main motivation the obvious link the Juche-ideology has with communism. The thing these people do not realise is that Cho Man-sik, although opposed to Soviet-Communism, was himself a (Christian) Communist. Furthermore, Cho Man-sik's own philosophy was not far removed from the Juche-ideology. Juche is often translated as “spirit of independence” or “self-reliance.” Cho Man-sik is well known for having advocated not only independence, but also “self-sufficiency”; in other words, that the state should be autonomous, not requiring any outside support for its survival. This is practically the same as the Juche-ideology which Kim Il-sung summarised as: (1) independence in political work, (2) self-sustenance in economic endeavours, and (3) self-defence in national defence.
The idea of self-sufficiency / self-reliance is present in both the term Juche and, by association, in the name Kodang. Choosing the name Kodang over Juche because you think the latter is associated with communism while the former is not only reveals your ignorance of Cho Man-sik's life. No, both “Juche” and “Kodang” has communist overtones.
I'm not claiming that there exists no political nuance to the name Juche. In the ITF dojang where I train in South Korea the names of all the patterns, including their explanations, are boldly displayed on a gigantic board. All, except one. The pattern Juche is completely left out on this display since its inclusion may cause suspicion of North-Korean sympathies, which is absolutely not the case. So clearly this name is politically charged.
While political nuances exist, I personally feel no discomfort practising Juche because I prefer to interpret the name somewhat literally. Looking at the Chinese characters we see that it is made up of two concepts. The first is 主, which means master or owner; the second is 體, with the denotative meaning of human body. To “master the body” is one of the main ambitions of the martial arts. Through years of devoted practise and discipline it is our aim to completely master our bodies, just like an artist aims to become the master of his medium of choice, be it paint or clay. My personal reading of the term Juche is therefore a wholly literal one, devoid of politics. And I think the name quite fitting to this pattern which is so physically demanding. It definitely requires the mastery of one's body to perform it skillfully.
Neither do I have any discomfort with practising the pattern Kodang. Cho Man-sik was an admirable man. He was an educator and helped establish several schools and universities, and a moral leader and philosopher who became known as the “Ghandi of Korea” because of his struggle for Korean independence from the Japanese occupation. Admittedly, because Kodang Teul is not part of the official 24 Chang-Hong patterns any more, I don't practise it that often—still, at least I have learned it and still perform Kodang Teul on occasion. In the same way, the two exercises Saju-Jjireukgi and Saju-Makgi are also not official patterns either and fall outside of the twenty-four pattern set, yet many people consider them as patterns and practise them as such. As for the claim that Juche Teul substituted Kodang Teul because of techniques, I'm gullible to believe this. Kodang Teul and Juche Teul clearly cover some of the same material. These two patterns share a number of unique motions that were not introduced in any of the earlier patterns; for instance the waist block, the downward elbow block, the hooking kick, the one-legged ready stance with back kick combination, and the twin knife-hand inward strikes. Juche Teul covers these techniques, plus a couple of extra novel movements. Both patterns also move backwards, unlike most other patterns that progress forwards. Juche Teul teaches what Kodang Teul teaches, plus more, so it does seem to be the case that this pattern was designed as a replacement for Kodang with some augmented material.
I do not think the move to rename Juche with Kodang (a seperate pattern) was a smart move and am in partial agreement with others (see here) who think that it will only cause confusion since there are now two patterns with the same name and that if they so strongly felt that a name change was necessary, a wholly new name for Juche would have been much better.
Kodang
Juche
