The fighting in Syria is not likely to end until there is a decisive victory by either the Alawite Syrian government or by the forces fighting to replace it. A stable division of the country along ethnic or sectarian lines, although perhaps desirable, seems unlikely.
Neither victory is very desirable from an Israeli or humanitarian point of view although there are some benefits to Israel from a long internal war in Syria. Israel probably would gain from having a divided Syria in which the Golan was only one of a number of areas removed from the control, or even sovereignty, of the central government. However, this seems unlikely.
If the revolutionary regime in Iran is overthrown, Israel would probably prefer an Alawite victory to one by the MB. But the Alawites are unlikely to be able to win without the support of the fanatic regime in Iran. So long as that regime rules Iran Israel should probably prefer continued war or a Sunni victory because they weaken Iran and Hesbollah.
While it is uncomfortable to be in any way supportive of a regime as murderous as Assad's, it doesn't seem likely that a Sunni regime would kill many fewer Syrians than Assad has and will. Whoever helps Assad's opponents is likely to have helped bring to power a force that slaughters hundreds or thousands of innocent civilians even after victory. Assad at least had the advantage of wanting to preserve the other minorities to help balance the Sunnis. The Sunnis, particularly after a long, nasty war, don't seem likely to produce a benign regime. All the minorities are afraid of the Sunnis, and with good cause as evidenced by what Sunni groups have done to minorities in Iraq and Egypt in the last few years.
Unless the Syrian government is able to win without using chemical weapons it seems likely to try to use those weapons before letting itself be defeated. Facing death of themselves and their families what would lead them to refrain from using chemical weapons? This will produce much hand-wringing in the "civilized" world, but it is hard to see anyone with the will and ability to do anything about it.
Chemical weapons are not in the same league as nuclear or biological weapons. They are not substantially more effective except perhaps in some special cases than explosive weapons. (Although many people feel that it is more unpleasant to face poison gas than artillery and bombs.) Therefore neither the US nor Israel probably the only countries with the ability to try to seize the weapons is likely to be strongly enough motivated to overcome the reluctance to put troops into Syria to take them which would in any case be difficult to do.
Perhaps the only scenario that would protect against the diversion of the chemical weapons (apart from a government victory) is if the US made a deal with the government to give it enough support against the rebels to win, in return for removal of the chemical weapons from Syria. While this might make some kind of sense it involves many problems and disadvantages and seems quite unlikely.
There is not much good news here. Except that Israel gets some benefit while the fighting continues. There is not much that Israel can do to affect the outcome. All it can do is to prepare to physically protect itself from the results, and to use the evidence the war provides to increase understanding of what Israel faces.
Israel has probably already gained some benefit, and will gain more, by the war's demonstration of how wise it has been not to deliver the Golan to Syria. (That is, how lucky it is that none of its efforts to trade the Golan for a peace agreement were accepted by the Syrians.) And the case for keeping the Golan may grow stronger as events suggest that Syria is not such a real country that it is entitled to get back whatever it once had for only 47 years. Nor is it a country that can be relied on to deliver peace for very long.
Some potential developments in Syria might provide an opportunity for Israel to assert a basis for permanently adding the part of the Golan it now has into Israel's permanent borders.