Gavrilo Princip 

This event is going to weaken Erdogan even more, when he is already weak at the national level. A weaker Erdogan can be taken out easily and replaced by more anti-russians authorities. And Lord knows the anti-russian feeling is prevalent in Turkey.
Putin already have a weak Erdogan; a weaker Erdogan is not in Putin's interest.
Also, this assassination may put Putin in a weird situation back home : he already let the l-killing of the pilot go, now this. It will be hard for him to justify the reinforcement of his ties with Turkey when Turkey is humiliating Russia by killing its soldiers and officials.
Are the rebels and their families still stuck in East Aleppo ?
Money talks. Both countries being isolated from each other serves no economic benefit.
The Russians are a major trade partner and the sanctions devastated large sectors of the economy. Turkey depends on Iranian and Russian oil and gas for energy. It gets cheap oil and gas from them and they cannot afford Qatari or American LNG imports.
If they cut off the gas, the Turkish economy goes straight to hell.
Putin basically understands this even though Russian views of Turkey have become negative. Russia removed the sanctions, and pumping money into Turkey to keep it afloat. China and Russia hardly do anything major alone anymore, there are large Chinese funds available for Turkey. They want to keep Turkey alive for the future. If they can wean the Turkish economy off the hot money, supply them with cheap oil, build the nuclear plants as agreed. Then Turkey might in the future be strong enough to leave its master and become an independent country and be part of that New Silk Road project.
A lot of buses have been taking them to Idlib today after the terrorist attack on buses yesterday. There are also Shia villages being evacuated in parallel with this evacuation.
The rapprochement between Russia and Turkey is mainly a move by Erdogan. He's basically on his own with that one. Turkey is a very divided country. Don't underestimate the will of some people within the turkish power to take out Erdogan and the hate many Turks have for Russia.
The reconciliation between the two countries is not seen as a good thing by everybody in Turkey. Russia is destroying a Sunni muslim take over in Syria. Some people are very mad about it. Even in the AKP, some people don't like the fact that Erdogan is now "buddy" with Russia.