Why do you think burying it deeper would kill it? If it was necessary to waterproof it, I don't think it would work. There are some plants that don't like to be buried any deeper, but I think those are the exception rather than the rule. For example, if it was grafted, as for many fruit trees, it would be important to keep the graft above ground. But tell us what it is, and maybe someone can say definitively yea or nay.