Ya, almond oil is safe. But more than this, I think you should correct her habit. She is quite young and this can be corrected else when they grow up it becomes hard and they do those things more, which they are told not to.
Since, she would be touching so many things, and may get infection if she sucks her thumb.
http://oilypedia.com/almond-oil-for-babies-pros-and-cons/
http://www.webmd.com/baby/features/breaking-thumb-sucking-habit
http://www.webmd.com/parenting/features/9-ways-to-wean-a-child-off-thumb-sucking