What if you just left the existing hole unfilled, and drilled a new LED hole on the side of the chassis where you wanted to have it?
Welcome to the joys of amp building! Everyone has made mistakes like this. Then each had to make the choice of whether to whether to start over from scratch, accept a cosmetic defect for better operation, or roll with a mistake and possibly compound it.
When I started out, I tried to force the mistake to work, which usually didn't turn out well. Now, I just accept the cosmetic defect instead of starting over. Every time, I've learned about something I overlooked, which improved subsequent builds.
Alternatively, you could try using the LED where it is. Original Standel amps had a light-up faceplate by having a 6.3vac pilot light at each end of the faceplate, putting one close to the input jack. Apparently, they didn't run into hum problems, and you might not either.
The question is whether you have an exit-strategy if you find you get hum/interference. Do you need a pilot light? Are you willing to leave the empty hole if you have to yank out the LED near the input jack? Will you then want to relocate that LED?
If you think you will still want the LED if it doesn't work in the present location, you may want to drill the better location now. It's always easier to drill an empty, incomplete chassis.
So you'll have to think through the "What If" and decide what works for you. And maybe you'll get lucky with what you have now.