All of the books I have been reading on pond construction would
indicate that this is totally possible to do on top of the liner. They
show the use of a second layer of liner under the pier for the stepping
stone like this:

_________
| | - Your "stepping stone"
----------------------------------------------------------- -
Waterline
| |
| |
| | - bricks or stone or whatever (cement and cinder
blocks would be good)
| |
| |
_ |_______|_____ - Extra layer of liner
________________________________________ - Pond Liner


You can also use a scrap of old carpet between the two layers of liner
for added cushion or below the overall liner as well.

While you *could* stretch the liner to cover the piers, this would add
a lot of "wasted" liner surface (and be expensive and probably fairly
ugly as well...