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I don't think you should remove the system cmake. This will only lead to the problems you described. Instead, you could simply install your own version of cmake and let it override the system cmake.
cd ~/Downloads/cmake-3.12.0-rc3/ # or wherever you downloaded cmake
./bootstrap --prefix=$HOME/cmake-install
make
make install
export PATH=$HOME/cmake-install/bin:$PATH
export CMAKE_PREFIX_PATH=$HOME/cmake-install:$CMAKE_PREFIX_PATH
The two export lines make sure that your updated cmake is used instead of the system cmake. You have to make sure that those lines are executed whenever you want to use the updated cmake. It's probably a good idea to put them into your .bashrc.
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