If your marriage was registered at the Ministry of Interior and you have completed the 5 year process of phased citizenship, and have become an Israeli citizen, then you should not be at risk, if you divorce. If you are within the process,and have either full custody or joint custody over your children, then your chances of remaining in Israel should be reasonably good. Clearly, the more co-operative your husband is, the greater your chances of remaining in Israel, with the children, if this is what you wish.
It would be wise to seek individual professional legal advice, and discuss the possibility of drawing up a separation or divorce agreement with your husband,if he is co-operative. The ideal would be to reach a court authorized agreement,at the appropriate time, which would ensure that you are the sole custodian, with him having generous visitation, or that there is shared and equal parenting in a joint custody arrangement. In either of these two scenarios it would be in the children’s interest that you would remain in Israel, so that they could have the opportunity of growing up knowing both of their biological parents. Should the Ministry of Interior not respect such an arrangement, regarding your status, and seek to order your expulsion, you could bring legal action at the District Court’s special court of administrative matters.