There are two issues:
Probably, you are referring to non-CafeTran project where ProjectTM is open if it exits in the same folder as such a non-native project. Just remove the ProjectTM.tmx from that folder.
Normally, the TM options dialog does not open when you load the memory automatically with the project. It does open, if CafeTran detects language pair mismatch between project and TM to let you match the languages.
Although I prefer to have it short, "Remove from project" would be a better naming than "Remove".