Given the date of this question, it was asked before "The Big Update" which removed this issue, but moreover completely revamped the game. To play as it was at the time of the question, one can still go back to cookie clicker classic.
In the update log of cookie clicker classic, you should note that the very next day, in version 0.125, an option to disable flashing was added. To prevent flashing, simply update to the newest version of cookie clicker classic (refresh the page) or upgrade to the entirely revamped cookie clicker where this is not an issue.
According to the source code in 0.125, this will affect the elder pledge:
if (Cookies>=1000000 && Pledge<=0 && Flashing)
{
var r=(Cookies-1000000)/2000000;
var r2=Math.max(0,(Cookies-100000000)/400000000);
var icon='grandmaicon';
if (Cookies>=2000000)
{
l('buyElder Pledge').style.display='block';
if (Math.random()<0.02) icon='grandmaiconinvert';
else if (Math.random()<0.02) icon='grandmaiconlustful';
}
if (Cookies>=10000000 && Math.random()<0.02) icon='skellington';
if (Cookies>=1000000000) l('whole').style.background='url(kaleigrandma.png) '+Math.floor(T*0.2)+'px -'+Math.floor(T*0.1)+'px';
else if (Math.random()<r)
{
l('whole').style.background='url('+icon+'.png) '+Math.floor(Math.random()*4)+'px '+Math.floor(Math.random()*4)+'px';
l('whole').style.backgroundSize=Math.floor(r2*Math.random()*64+64)+'px '+Math.floor(r2*Math.random()*64+64)+'px ';
}
}//sorry
else l('whole').style.background='#ccc';
As noted in the if statement, turning off flashing will disable the whole of the grandmapocalypse. Also, as this is in the main function, it should not be dependent upon any clicking and should happen on its own - perhaps it coincided with your clicks due to your browser or simply by coincidenced.
You need to have Cookie Clicker as your active tab to let Raptr track your gametime and the browser doesn't need to have focus. If you're browsing with multiple tabs, everytime you switch out from Cookie Clicker, Raptr will notify you something like 'Cookie Clicker - 9 seconds played'.
This behavior has been tested with Chrome and Firefox. With Explorer I'm under the impression that gametime isn't tracked at all.
Best Answer
There is only one other way to stop the grandmapocolypse: selling all your Grandmas. This lasts until you rebuy one.
Another way out would be ascending and not buying the "One mind" upgrade in the next game.