When I started in the Auto trade, we used to rebuild calipers all the time. To replace that boot, you will need to remove the caliper, remove the piston, remove the boot & reassemble. If you haven't done it before, it may not be much fun as it takes practice & patience to get the piston back in without damage to your new boot. (there are tricks to do it, but it involves a large volume of compressed air & some practice) Can you even buy the boots separately ???
As Fummins says, yes it's safe. That seal keeps dust & debris away from the piston. The fluid is sealed by a square "O" ring further in the caliper.. You may be just as far ahead to run it as it is...Depending on your climate, they may last forever!!!