Step 1 would be to stop undermining them
What good is it for Israel to negotiate a deal with Abbas, or the Lebanese government if they are too weak to control their territory? Any agreement is not worth the paper that it is written on. The Palestinians and the Lebanese need to make a strategic decision to have 1 powerful central government and enforce it even if it comes to civil war. Until then there will be no solution.
You are right that negotiating with the weak PA or Lebanese government is of limited value, they don't have the power to stop all attacks. But Israel has gone to great lengths to keep either country from developing a strong government for fear that such a government would be a foe of Israel.
A permanent solution to the problem requires a government strong enough to control the country. Israel needs to accept that and encourage the formation of strong governments, even though doing so will mean over the short term surrounding themselves with enemies.
Jay