Are the Israeli Police allowed to go up to the mosque (if they dont go inside it) to fight back agressors (which is what happened today)?

Yes, they may go up to the mosque, because the rioting and agression is considered a 'pikuach nefesh', danger to life. However, it is preferable for a religious soldier to go because there are halachot that one has to know such as doing tevila (ritual immersion in a mikvah), not staying in the area longer than necessary, and other halachot. (see Rav Yosef Shalom Elyahiv's responsa in Kav V'naki, 1:692, and Rav Avigdor Nebenzal's responsa in Kuntres Hahanhagot at the end of his commentary on the Mishna Berura, 29).