How to disable cron from running while another time consuming process takes place?
You can use Elysia Cron. This module is a enhanced Cron that has, apart of many other improvements, a global disable option. As they say in a bug report this variable may help you:


  It disables ALL cron tasks. (No cron will be executed).


Also Elysia Cron allows you to set complex schedules so you may fix your problem just with the right schedule.