The official Israeli stance on Syria is that all the rebels and the Syrian government are different shades of trouble for Israel but it maintains a posture of overall neutrality. That said it has a clear strategic interest in denying Iran a forward base against Israel in Syria under the protection of the Assad regime. So most Israeli strikes inside a country that it is technically still at war with have been with that in mind. It would be better if Assad and Iran did not emerge as clear victors in this conflict but Israel has no interest in blessing Daesh either. At the same time extensive humanitarian aid has been given by Israel to more than 200000 Syrian civilians. That some of these may have included injured members of the Free Syrian army is speculated and would fit the interest of Israel in support of a more moderate but less Islamist force toppling the Assad regime without opening up Syria to the prospect of a later Islamist victory. More likely than not Assad will come out on top of this conflict and Israel will find itself directly opposed to Assad and Iran/Hezbollah as has been its default position for most of the last decades. Syrian weakness and division is meanwhile a blessing to Israel in that the country is no longer a direct military threat.
Personally I regard Assad as better for the preservation of the church but have no desire that he be in the same position of strength he was before the civil war because of the threat he poses to Israel. The Iranian connection is probably a weakening factor in the long run for this regime as the majority of his population are Sunnis. The Israelis appear to trust Saudi or Turkish influence over Iranian influence in Syria but these are not so clearly better in any objective sense for the preservation of the church or indeed for the stability and well being of the region. So while I understand Israeli opposition to Iran it is not necessarily to their strategic advantage to rid the country of them. Syria will be weaker if Iran remains. Of course that does not rule out Israel managing direct threats to its security on a case by case basis.
Israeli involvement in the Syrian Civil War - Wikipedia
