When you install a waterblock (hoping that you get a good one, not a boxed all-in-one kit) you will get retention brackets and usually a backplate. With that, you can tighten down the block without it putting stress on the board because the bracket is designed to bear the flex load instead of the MB PCB. Even then, you don't want to apply too much pressure, but PCB is designed to flex.
If you have your chip mounted correctly and the stock cooler is oriented correctly (which really, is any direction) you should be fine. Most of the time that you get push pin coolers, you will see some PCB flex like this...its pretty common. Look at graphics cards; they often begin to bend after just a month or 2 from the weight of the copper in the heatsinks as well as the high amount of heat radiating through the board. With a stock cooler or one with pushpins, you really can't go wrong mounting it, unless you don't get the pins inserted all the way. ...or you have your CPU mounted wrong which would have been obvious when it didn't sit in the socket correctly.