No problem....it will NOT be less secure . Typically tapered pins so just drive them to the original depth
Key thing to remember is have a good punch ( Starett for example ). Just be carefull because most punches have flat bottom. A concave punch ( nail set ) is sometimes nice since it doesn't skate off and scratch your gas block / sight
Most are pins drive out from left to right. Notable exceptions are Stag and S&W MP15s that drive out right to left
I have a brownells jig...the best $30 I ever spent . It cradles the front sight perfectly and even has two faces...one that is clearly marked "pins out" and other " pins in" ...no thinking required
Even if you block with 2X4 or other wood , upper will roll. Best to have someone hold it for you