It's not ideal, but it'll work. It will obviously be louder and have more recoil the what most use to shoot yotes, but it's really up to you. The hard part will be finding ammunition that will fragment instead of passing through and creating another hole. I'm not aware of any myself. .30-06 is a lot bigger than is traditionally used on coyotes, so they don't really make rounds geared towards it in that caliber. If it's what you have available though, and what you want to use, it'll kill 'em if you hit 'em right.
2009/10 Season Totals:
and my very first deer, should have done it decades ago