I was also trying to think of another way to justify Shaak Ti's actions... The Jedi are often/usually loyal to their mandate from the council to a fault. For example, Qui-Gon first refused to try to free Anakin and his mother from slavery during TPM, because they "were not sent to free slaves", even though it was the right thing to do. Obi-Wan also chastises Anakin during AOTC when he over-steps the council's mandate and tells Padme that they will find who is attempting to assassinate her, instead of just protecting her.
However, Shaak Ti doesn't even fall into this category, since her mandate was to protect the Jedi Temple.
Originally Posted by Wookieepedia
Shaak Ti was selected to safeguard the Jedi Temple while Mace Windu took a group of Jedi Masters to arrest the Supreme Chancellor.