Is it safe to convert a shunted tombstone lamp socket to a non-shunted socket by cutting the shunt?
You can't hack a shunted lampholder to be a non-shunted unless it's designed to do that.  For one thing there is no place to attach the wires. Yes, there are two wire holes, but a non-shunted holder has four.  

You have three options: 


stay with instant-start fluorescent... I am because the CRI is better
change lampholders to non-shunted type
take care to select LED "tubes" which take power from opposite ends of the tube


You should certainly not be modifying the wiring before you have seen the wiring diagram which comes with your LED tubes.  You may find your tubes require a different wiring than what you did.