I too have heard that limestone is not a good choice for a pond however all the rocks around my pond are limestone. The rock shelf goes right into the water and the waterfall is made of three large pieces of limestone so water is always in contact with or flowing over the limestone rock of my pond. The pea gravel in the large gravel filter/bog area for the pond is also limestone. I have not noted any ill effects to plants or fish. My pond is about 9 years old. The rainfall around here tends to be on the acidic side so the limestone does have a buffering effect which may be why it works for me.
Not sure how my pond compares to yours but for me limestone seems to be alright.
emm