The only issue with silicone is that it will make it harder to refinish the guitar if you ever want to have it refinished.
The guitar would have to be stripped totally. Most polishes will have silicone in them. Being in the auto restoration hobby, you get used to all the prep you have to do before painting to remove all traces of silicone. Otherwise you will get fisheyes in the paint That includes interior dyes. Armor All is the worst.
Something with a micro abrasive, and then a good Carnuba wax over it will do wonders. Actually if the scratch is not "too" deep a good coat of wax will take care of it.