There's not much counterplay to a Nuke Atlas blowing up in your face for massive damage the moment you doom it, so take advantage of its destructive power. If the enemy commander fields all his Titans at once, drop a lone Nuke Atlas and sacrifice it to significantly damage them all before sending your cleanup crew. It works just as well when taking out Medium Turrets. It should be noted that the Nuke Atlas will ignore enemy infantry.
Before Patch 2.1.1, there was no counterplay to a Nuke Atlas about to explode. However, currently (as well as before October 26 when this bug was introduced) BT-7274 or a charged Core Ronin can Terminate on the Nuke Atlas when it falls under a Doomed State, preventing it from blowing up. After said patch is installed, BT is no longer able to terminate the Nuke Atlas.