If you walk through any precious stone, for example the jack o death or glow of life you can negate its effects by holding shift and crouching through the area. It is possible that after holding shift for a very long time in a precious stones field it will start effecting you but this seems to rarely happen.

Is it at all possible to prevent a user form holding shift to negate a stones effects?

Yes, you can toggle the sneaking-bypasses-damage flag in the config.

This is a feature not a bug. Maybe it could be enabled via a flag rather than always being on.