These incidents are isolated to places like Anantnag, Shopian, Baramulla, Sopore, Bandipora and Sonamarg. Rest of Kashmir & Jammu is relatively safe.
If your plan is just going to Ladak & Leh, it better to take route via Manali. Leh is almost 14hr drive from Manali.
Just don't try anything that might attract attention and if you are travelling with women ask them to dress conservatively.