Is it permissible to take some books that promote misguidance from Sufi mosques and destroy them or keep them to present to scholars, or is that considered theft?

If the books found in mosques are authored to support an innovation (bid'ah) or a reprehensible act (munkar), then it is permissible to destroy them. It may even become obligatory if no greater harm results from it. Ibn al-Qayyim mentioned the permissibility of burning and destroying misleading books, citing the Prophet's (peace be upon him) action with 'Umar when he threw a book from the Torah into the oven. The Companions also burned copies of the Qur'an that differed from the Mushaf of 'Uthman. Similarly, the Malikis, Shafi'is, and Hanbalis have issued fatwas permitting—and even obligating—the destruction of forbidden books, such as those on magic, disbelief (kufr), astrology, and philosophy.