How to or Is that possible to stop mDNSResponder without disable System Integrity Protection?
You cannot unload mDNSResponder on a standard setup with SIP enabled. You will have to disable SIP from Recovery mode in order to be able to do so. 

I would not recommend running with SIP permanently disabled, which would be necessary if you want to periodically unload/load mDNSResponder with launchctl. So if you really want to do this (relatively obscure) thing, then I suggest permanently unloading the launch daemon, and then manually starting/stopping mDNSResponder as needed. The latter can be done with SIP enabled.

A different way to approach the issue, assuming that network traffic is the cause of the wakes, could be to let mDNSResponder run all the time, and use the built-in firewall pf to block all traffic from mDNSResponder before going to sleep, and removing the block after it wakes. 

Yet another could be to take a look at the IOPlatformFeatureDefaults and check if TCPKeepAliveDuringSleep is enabled, and try disabling that. It could fix your problem potentially. You can find more information on how to do that here:

https://discussions.apple.com/message/30869802#30869802