Two things that I would worry about are 1) The roots of the tree eventually growing into your liner and either causing a leak or constricting the growth of the tree. 2) Japanese Maples do not tolerate wet soil, so if the pond overflow is not directed well away it will kill the tree.
Being that the tree is small, it might easily be relocated and offer up that area to make your pond larger, and the tree could be used as an accent nearby on higher ground. JMO