Some issues are legislative in nature, and to be voted upon by people. Some issues are executive in nature, and meant to be decided by professionals.
Lawmaking is legislative. But operational arrangements, like where the army should deploy itself, where each battallion should be based, where each division should be based etc are not issues which can be put to public vote - these are best decided by professionals. So whether the army should be in Kashmir or not is for the army and other security forces to decide, not by the general public in a referendum. What next, decide which aircraft to procure for our MRCA by a popularity contest?
And by the way, the army is not deployed in Kashmir, only the Rashtriya Rifles are. They are drawn from the army, but they are an exclusive counter insurgency force that does not use heavy weapons, or anything that might cause hardship to the general public. What difference does it make to Kashmiris, whether it is the RR or police forces that tackle militancy? It makes a difference to India in general, since the RR are extremely capable, and professional.